Protein Name Entry Number No. of Data Reference Remarks
Old New
c-Myb protein 1-47 1-42 42 J MOL BIOL. 1998; 276: 571-590 PMID: 9551098 5 deleted
cI repressor 48-62 43-57 15 BIOCHEMISTRY. 1995; 34: 8554-8563 PMID: 7612597  
Trp repressor 63-67 58-62 5 BIOCHEMISTRY. 1993; 32: 7302-7309 PMID: 8343520  
Met repressor 68-80 63-75 13 BIOCHEMISTRY. 1995; 34: 3212-3221 PMID: 7880815  
MAT alpha2 protein 81-85 76-80 5 BIOCHEMISTRY. 1997; 36: 526-535 PMID: 9012668  
Arc repressor 86-88 DD   PROC NATL ACAD SCI U S A. 1994; 91: 8244-8247 PMID: 8058788 3 deleted
Lac repressor 89-101 81-93 13 BIOCHEMISTRY. 1999; 38: 3579-3590 PMID: 10090744  
Cro repressor 102-189 94-181 88 PROC NATL ACAD SCI U S A. 1989; 86: 439-443 PMID: 2911590  
Cro repressor 190-209 182-201 20 PROC NATL ACAD SCI U S A. 1992; 89: 8180-4 PMID: 1518844  
GCN4 protein 210-227 202-219 18 BIOCHEMISTRY. 1996; 35: 14984-91 PMID: 8942664  
cI repressor 228-279 220-271 52 PROC NATL ACAD SCI U S A. 1989; 86: 6513-7 PMID: 2771938  
c-Myb protein 280-312 272-304 33 PROC NATL ACAD SCI U S A. 1993; 90: 9320-9324 PMID: 8415700  
c-Myb protein 313-354 305-346 42 NAT STRUCT BIOL. 1996; 3: 178-187 PMID: 8564545  
bZIP peptide 355-386 347-378 32 BIOCHEMISTRY. 1997; 36: 15349-15355 PMID: 9398264  
cAMP receptor protein 387-412 379-404 26 J BIOL CHEM. 1999; 274: 6946-6956 PMID: 10066748  
Glucocorticoid receptor 413-425 405-417 13 BIOCHEMISTRY. 1993; 32: 5074-5082 PMID: 8494884  
T7 RNA polymerase 426-431 418-422 5 BIOCHEMISTRY. 1996; 35: 14574-14582 PMID: 8931555 1 deleted
Immunoglobulin IgG (Jel 274) 432-437 423-428 6 NUCLEIC ACIDS RES. 1997; 25: 1442-1449 PMID: 9060442  
Glucocorticoid receptor 438-460 429-451 23 PROC NATL ACAD SCI U S A. 1996; 93: 4754-94754-9 PMID: 8643475  
Trp repressor 461-474 452-465 14 J MOL BIOL. 1994; 238: 669-681 PMID: 8182742  
Tus protein 475-499 466-489 24 J BIOL CHEM. 1995; 270: 28049-28054 PMID: 7499290 1 deleted
Sso7d protein 500-519 490-510 21 J MOL BIOL. 1998; 276: 775-786 PMID: 9500918 1 added
NF-kappa-B p50 520-527 511-516 6 NUCLEIC ACIDS RES. 1999; 27: 1063-1069 PMID: 9927740 2 deleted
cI repressor 528-541 517-530 14 BIOCHEMISTRY. 1997; 36: 12994-13003 PMID: 9335560  
Sox-5 protein 542-567 531-556 26 J MOL BIOL. 1999; 294: 997-1013 PMID: 10588902  
hGBP1 protein 568-584 DD   J MOL BIOL. 1999; 292: 321-332 17 deleted
Glucocorticoid receptor 585-638 557-584 28 BIOCHEMISTRY. 1994; 33: 5955-5965 PMID: 8180225 26 deleted
PU.1 protein 639-650 585-590 6 PROTEIN SCI. 1999; 8: 2098-2109 PMID: 10548056 6 deleted
Lac repressor 651-724 591-656 66 J MOL BIOL. 1997; 267: 1186-1206 PMID: 9150406 8 deleted
ss DNA binding protein 725-775 657-707 51 BIOCHEMISTRY. 1994; 33: 12896-12910 PMID: 7947696  
MASH-1 protein 776-797 708-727 20 BIOCHEMISTRY. 1998; 37: 4217-4223 PMID: 9521744 2 deleted
Lac repressor 798-819 728-749 22 BIOCHEMISTRY. 1993; 32: 11374-11384 PMID: 8218202  
Cellular tumor antigen p53 820-824 750-754 5 J BIOL CHEM. 1997; 272: 14842-14849 PMID: 9169453  
PU.1 protein 825-882 755-797 43 BIOCHEMISTRY. 1998; 37: 9802-9811 PMID: 9657694 15 deleted
Interferon regulatory factor 4   798-812 15 BIOCHEMISTRY. 1998; 37: 9802-9811 PMID: 9657694 15 added
Estrogen receptor 883-894 DD   J Biol Chem. 1997 Nov 28;272(48):30405-11 12 deleted
ss DNA binding protein 895-1006 813-924 112 BIOCHEMISTRY. 1999; 38: 7388-7397 PMID: 10353851  
cI repressor 1007-1045 925-963 39 BIOCHEMISTRY. 1992; 31: 57-65 PMID: 1531023  
Ethylene-responsive element-binding factor 1046-1107 964-1039 76 J BIOL CHEM. 1998; 273: 26857-61 PMID: 9756931 14 added
c-Myb protein 1108-1138 1040-1068 29 FEBS Lett. 1999; 454: 288-92 PMID: 10431824 2 deleted
Trp repressor 1139-1173 1069-1099 31 J MOL BIOL. 1999; 287: 539-54 PMID: 10092458 4 deleted
Gal repressor 1174-1193 1100-1115 16 BIOCHEMISTRY. 1990; 29: 3374-3383 PMID: 2185837 4 deleted
ss DNA binding protein 1194-1294 1116-1210 95 J MOL BIOL. 1998; 278: 999-1014 PMID: 9600857 6 deleted
c-Myb protein 1295-1296 1211-1212 2 BIOCHEMISTRY. 1993; 32: 7759-7764 PMID: 8347585  
T4 gene 32 protein 1297-1310 1213-1226 14 BIOCHEMISTRY. 1989; 28: 7409-7417 PMID: 2684276  
I-PpoI endonuclease 1311-1323 1227-1239 13 BIOCHEMISTRY. 1996; 35: 1076-1083 PMID: 8547243  
Purine repressor 1324-1326 1240-1242 3 J BIOL CHEM. 1998; 273: 8958-8964 PMID: 9535880  
c-Myb protein 1327-1362 1243-1278 36 PROTEIN ENG. 1997; 10: 1407-1414 PMID: 9543002  
cI repressor 1363-1386 1279-1304 26 J MOL BIOL. 1986; 192: 27-38 PMID: 2950238 2 added
TyrR protein 1387-1419 1305-1337 33 BIOCHEMISTRY. 1998; 37: 7431-7443 PMID: 9585557  
Trp repressor 1420-1439 1338-1357 20 J MOL BIOL. 1997; 273: 572-585 PMID: 9356247  
E2 protein 1440-1449 1358-1367 10 BIOCHEMISTRY. 1996; 35: 9864-9872 PMID: 8703960  
Arc repressor 1450-1453 1368-1371 4 PROC NATL ACAD SCI U S A. 1999; 96: 811-817 PMID: 9927650  
c-Myb protein 1454-1501 1372-1419 48 J BIOL CHEM. 1997; 272: 17966-17971 PMID: 9543002  
ss DNA binding protein 1502-1507 1420-1425 6 BIOCHEMISTRY. 1996; 35: 5272-5279 PMID: 8611514  
uvsY protein 1508-1512 1426-1435 10 J MOL BIOL. 1997; 266: 927-938 PMID: 9086271 5 added
Immunoglobulin IgG 1513-1520 1436-1443 8 J BIOL CHEM. 1996; 271: 12241-12246 PMID: 8647821  
HMGB1 protein 1521-1531 1444-1454 11 PROTEIN ENG. 1999; 12: 235-242 PMID: 10235624  
HMGB2 protein 1532-1538 1455-1461 7 BIOCHEMISTRY. 1999; 38: 589-595 PMID: 9888798  
cI repressor 1539-1542 1462-1465 4 J MOL BIOL. 1998; 282: 947-958 PMID: 9753546  
TATA binding Protein 1543-1547 1466-1470 5 BIOCHEMISTRY. 1998; 37: 15842-15849 PMID: 9843390  
Sac7d protein 1548-1567 1471-1490 20 BIOCHEMISTRY. 1996; 35: 4034-4045 PMID: 8672437  
EcoRV endonuclease 1568-1572 1491-1495 5 Biochemistry. 1999 Jun 29;38(26):8430-9  
EcoRV endonuclease 1573-1577 1496-1500 5 Nat Struct Biol 1999 Mar;6(3):269-77  
EcoRV endonuclease 1578-1591 1501-1514 14 Biochemistry. 1999 Jun 29;38(26):8430-9  
Androgen receptor 1592 1515 1 Biochemistry. 1999 Jul 27;38(30):9718-27  
Glucocorticoid receptor 1593-1595 1516-1518 3 Biochemistry. 1990 Jun 5;29(22):5358-64  
OmpR protein 1596-1618 1519-1541 23 J Mol Biol. 1998 Sep 4;281(5):857-70  
OmpR protein 1619-1633 1542-1556 15 J Mol Biol. 2000 Jun 23;299(5):1257-70  
TATA binding protein 1634-1676 1557-1599 43 Biochemistry 2001 Feb 27;40(8):2419-25  
TATA binding protein 1677-1685 1600-1608 9 Biochemistry. 2000 Jul 18;39(28):8259-65  
Tn916 integrase 1686-1712 1609-1635 27 J Mol Biol. 2000 Jul 21;300(4):841-56  
Transcription factor IIIA 1713-1726 1636-1644 9 Proteins 2000 Suppl 4:50-62 5 deleted
NF-kappa-B p50 1727-1745 1645-1663 19 J Biol Chem. 2000 Aug 11;275(32):24392-9  
GCN4 protein 1746-1752 1664-1670 7 Biochemistry. 2000 May 30;39(21):6380-9  
ss DNA binding protein 1753-1755 1671-1673 3 J Mol Biol. 2000 Mar 3;296(4):989-99  
Replicative helicase PriA 1756-1767 1674-1685 12 Biochemistry. 2000 Aug 29;39(34):10454-67  
Major cold shock protein CspB 1768-1772 1686-1690 5 J Biol Chem. 1999 Nov 19;274(47):33601-8  
Mnt repressor 1773-1787 1691-1705 15 J Mol Biol. 2000 Aug 25;301(4):959-73  
BamHI endonuclease 1788-1848 1706-1766 61 J Mol Biol. 2001 Mar 23;307(2):619-36  
MASH-1 protein 1849-1860 1767-1778 12 Nucleic Acids Res. 2000 May 15;28(10):2122-7  
Oct-1 protein 1861-1883 1779-1801 23 Biochemistry. 2000 Jun 27;39(25):7570-9  
Trp repressor 1884-1922 1802-1840 39 J Mol Biol. 2000 Jan 7;295(1):17-28  
Immunoglobulin IgG 1923-1973 1841-1891 51 Biochemistry. 1999 Nov 2;38(44):14631-7  
Tus protein 1974-1994 1892-1912 21 Biochemistry. 2000 Oct 3;39(39):11989-99  
TATA binding protein 1995-2000 1913-1918 6 J Biol Chem. 2001 May 4;276(18):14614-22  
Cellular tumor antigen p53 2001-2006 1919-1924 6 Biochemistry. 2001 Apr 3;40(13):3847-58  
EcoRV endonuclease 2007-2022 1925-1940 16 Biochemistry. 2001 Feb 27;40(8):2484-94  
Restriction enzyme EcoKI 2023-2042 1941-1960 20 J Mol Biol. 2001 Mar 30;307(3):951-63  
GCN4 protein 2043-2060 1961-1978 18 Biochemistry. 1999 Mar 30;38(13):4008-17  
Gal repressor 2061 1979 1 Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):2957-62  
TATA binding protein 2062-2068 1980-1986 7 J Biol Chem. 2001 May 4;276(18):14623-7  
uvsY protein 2069-2076 1987-1994 8 Biochemistry. 1999 Dec 14;38(50):16589-98  
NF-kappaB p50 2077 1995 1 J Biol Chem. 1991 Jan 5;266(1):252-60  
CopR repressor 2078-2081 1996-1999 4 Proteins. 2000 Mar 1;38(4):393-406  
Integration host factor 2082-2097 2000-2015 16 J Mol Biol. 2001 Jul 6;310(2):379-401  
Vsr endonuclease 2098-2106 2016-2024 9 J Mol Biol. 2001 Jul 13;310(3):501-8  
Purine repressor 2107-2117 2025-2035 11 Biochemistry. 2001 Jul 10;40(27):8109-17  
DNA gyrase 2118-2121 2036-2039 4 J Mol Biol. 2001 Jun 22;309(5):1219-31  
Cmb1 protein 2122-2136 2040-2054 15 J Mol Biol. 2001 Jun 22;309(5):1101-15  
Oct-1 protein 2137-2140 2055-2058 4 Biochemistry. 2001 Jun 5;40(22):6580-8  
TATA binding protein 2141-2184 DD   Biochemistry. 2001;40:2419-25 44 deleted
DNA topoisomerase II 2185-2187 2059-2061 3 J Biol Chem. 1999 Feb 5;274(6):3446-52  
DNAB helicase 2188-2190 2062-2064 3 Biochemistry. 1999 Aug 24;38(34):10929-39  
hnRNP core protein A1 2191-2217 2065-2091 27 Biochemistry. 1991 Mar 19;30(11):2968-76  
Deadpan protein 2218-2219 2092-2093 2 Biochemistry. 1999 Apr 20;38(16):5138-46  
PUMILIO 2220-2223 2094-2097 4 Biochemistry. 1999 Jan 12;38(2):596-604  
HU protein 2224-2247 2098-2121 24 J Mol Biol. 2001 Aug 17;311(3):491-502  
Adr1 protein 2248-2270 2122-2144 23 Biochemistry. 2000 Jan 25;39(3):567-74  
Arginine repressor 2271-2278 2145-2152 8 J Mol Biol. 2001 Oct 5;312(5):949-62  
ModE repressor 2279-2282 2153-2156 4 J Biol Chem. 1999 Aug 20;274(34):24308-15  
cAMP response element binding protein 2283-2300 2157-2174 18 J Biol Chem. 2001 Apr 13;276(15):11719-28  
GCN4 protein 2301 2175 1 Biochemistry. 2001 Nov 20;40(46):13833-9  
cAMP receptor protein 2302-2310 2176-2184 9 Biochemistry. 2001 Oct 16;40(41):12329-38  
Fli-1 protein 2311-2315 2185-2189 5 J Biol Chem. 2000 Sep 15;275(37):28363-70  
Sap-1 protein 2316-2321 2190-2195 6 J Biol Chem. 2000 Sep 15;275(37):28363-70  
PU.1 protein 2322-2327 2196-2201 6 J Biol Chem. 2000 Sep 15;275(37):28363-70  
MASH-1 protein 2328-2379 DD   Biochemistry. 1995 Sep 5;34(35):11026-36 52 deleted
TATA binding protein 2380-2398 2202-2220 19 J Mol Biol. 1998 May 29;279(1):117-25  
cAMP receptor protein 2399-2414 2221-2236 16 Nucleic Acids Res. 1989 Dec 25;17(24):10295-305  
Cellular tumor antigen p53 2415-2425 2237-2247 11 Biochemistry. 2002 Jan 8;41(1):170-8  
Transcription factor 1 2426-2495 2248-2317 70 J Mol Biol. 1996 Jul 12;260(2):196-206  
Integration host factor 2496-2509 2318-2331 14 J Mol Biol. 1996 Jul 12;260(2):120-5  
HU protein 2510-2515 2332-2337 6 J Mol Biol. 1996 Jul 12;260(2):120-5  
Gal repressor 2516 2338 1 Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):2957-62  
Lac repressor 2517-2520 2339-2342 4 Proc Natl Acad Sci U S A. 2001 May 22;98(11):6039-44  
Lac repressor 2521-2626 2343-2348 6 J Biol Chem. 1997 Oct 24;272(43):26818-21  
Lac repressor 2527-2611 2349-2433 85 Biochemistry. 2000 Sep 12;39(36):11074-83  
ss DNA binding protein 2612-2614 2434-2436 3 Biochemistry. 2002 May 14;41(19):6032-44  
Estrogen receptor 2615-2620 2437-2442 6 J Biol Chem. 1997 Nov 28;272(48):30405-11  
Estrogen receptor 2621-2642 2443-2464 22 Nucleic Acids Res. 2000 Jul 1;28(13):2494-502  
Hin recombinase 2643-2651 2465-2473 9 Protein Sci. 1996 Oct;5(10):2119-24  
Lac repressor 2652-2658 2474-2480 7 J Mol Biol. 1999 Jul 16;290(3):653-66  
PcaU protein 2659-2661 2481-2483 3 J Bacteriol. 2002 Apr;184(7):1988-97  
Fis protein 2662-2677 2484-2499 16 EMBO J. 1991 Jun;10(6):1593-603  
Regulatory factor RFX1 2678 2500 1 Nucleic Acids Res. 1998 May 1;26(9):2143-9  
XPC-HR23B complex 2679-2684 2501-2506 6 Biochemistry. 2002 May 28;41(21):6583-7  
CopR repressor 2685 2507 1 Nucleic Acids Res. 2002 May 1;30(9):2052-60  
Replication protein RepA 2686-2688 2508-2510 3 Biochemistry. 2001 Jun 19;40(24):7211-8  
GAGA protein 2689 2511 1 Proc Natl Acad Sci U S A. 1996 Apr 2;93(7):2822-6  
EcoP15I DNA methyltransferase 2690-2695 2512-2517 6 J Mol Biol. 2000 May 12;298(4):597-610  
Sox-9 protein 2696-2697 2518-2519 2 Nucleic Acids Res. 1999 Mar 1;27(5):1359-64  
Trp repressor 2698-2699 2520-2521 2 Nucleic Acids Res. 1987 Jul 10;15(13):5339-51  
Oct-1 protein 2700-2718 2522-2540 19 J Mol Biol. 1999 May 21;288(5):941-52  
Restriction enzyme EcoKI 2719-2744 2541-2565 25 EMBO J. 1998 Dec 1;17(23):7118-27 1 deleted
Replication protein A 2745-2748 2566-2569 4 J Biol Chem. 2002 May 3;277(18):16096-101  
Recombination protein RecA 2749-2750 2570-2571 2 J Biol Chem. 2002 May 3;277(18):16257-64  
TraM protein 2751-2756 2572-2577 6 J Biol Chem. 2002 May 10;277(19):16705-11  
NF1-C1 protein 2757-2759 2578-2580 3 J Biol Chem. 2002 May 10;277(19):16383-90  
Fis protein 2760-2778 2581-2599 19 J Mol Biol. 1996 Dec 13;264(4):675-95  
Fis protein 2779-2780 2600-2601 2 Biochemistry. 2002 May 7;41(18):5788-98  
MASH-1 protein 2781-2786 2602-2607 6 Nucleic Acids Res. 1998 Mar 15;26(6):1408-13  
MASH-1 protein 2787-2792 2608-2613 6 Biochemistry. 1997 Feb 4;36(5):1085-91  
DNA polymerase beta 2793-2795 2614-2616 3 Biochem J. 2002 Jan 15;361(Pt 2):317-25  
Myogenin 2796 2617 1 J Mol Biol. 2002 Mar 29;317(3):431-45  
GAGA protein 2797 DD   Proc Natl Acad Sci U S A. 1996 Apr 2;93(7):2822-6 1 deleted
ss DNA binding protein 2798-2805 2618-2625 8 Biochemistry. 1997 Jun 3;36(22):6732-8  
LexA repressor 2806-2807 2626-2627 2 Biochemistry. 1997 Feb 4;36(5):1077-84  
Elongation factor TUF 2808-2809 2628-2629 2 J Biol Chem. 1990 Aug 25;265(24):14669-74  
ORF56 protein 2810-2813 2630-2633 4 Nucleic Acids Res. 2001 Feb 15;29(4):904-13  
EcoRV endonuclease 2814-2819 2634-2639 6 Biochemistry. 1994 Feb 22;33(7):1812-9  
Met repressor 2820-2827 2640-2647 8 Nucleic Acids Res. 1995 Jan 25;23(2):211-6  
DREAM protein 2828-2833 2648-2653 6 J Biol Chem. 2001 Nov 2;276(44):41005-13  
Diphtheria toxin repressor 2834-2839 DD   Biochemistry. 2000 Aug 29;39(34):10397-407 6 deleted
Replicative helicase PriA 2840-2849 2654-2663 10 J Biol Chem. 2000 Sep 8;275(36):27865-73  
TATA binding protein 2850 2664 1 Biochemistry. 1995 Aug 8;34(31):9977-84  
PU.1 protein 2851-2880 2665-2694 30 Biochemistry. 2002 Feb 19;41(7):2361-71  
Restriction enzyme EcoKI 2881-2897 2695-2711 17 J Mol Biol. 1998 Nov 13;283(5):947-61  
Wilms tumor protein WT1 2898-2904 2712-2718 7 Biochemistry. 1998 Feb 17;37(7):2051-8  
Zif268 zinc finger protein 2905-2910 2719-2724 6 Biochemistry. 1998 Feb 17;37(7):2051-8  
Wilms tumor protein WT1 2911-2929 2725-2743 19 Biochemistry. 1998 Feb 17;37(7):2051-8  
Zif268 zinc finger protein 2930-2945 2744-2759 16 Biochemistry. 1998 Feb 17;37(7):2051-8  
McrBC protein 2946-2948 2760-2762 3 J Mol Biol. 2000 May 12;298(4):611-22  
Autoantigen protein Ku 2949-2952 2763-2766 4 Biochemistry. 2001 Aug 14;40(32):9638-46  
Autoantigen protein Ku 2953-2960 2767-2774 8 J Biol Chem. 2002 Mar 22;277(12):9741-9748  
Filamentous flower FIL 2961-2972 2775-2786 12 J Biol Chem. 2002 Apr 5;277(14):11957-64  
RNA polymerase T7 2973-2975 2787-2789 3 Biochemistry. 2002 Mar 19;41(11):3586-95  
CRT/DRE binding factor 1 2976-2991 2790-2805 16 Biochemistry. 2002 Apr 2;41(13):4202-8  
Ethylene responsive element binding factor-2 2992 2806 1 Biochemistry. 2002 Apr 2;41(13):4202-8  
CRT/DRE binding factor 1 2993 2807 1 Biochemistry. 2002 Apr 2;41(13):4202-8  
Ethylene responsive element binding factor-2 2994-2998 2808-2812 5 Biochemistry. 2002 Apr 2;41(13):4202-8  
Chimera CNEC 2999 2813 1 Biochemistry. 2002 Apr 2;41(13):4202-8  
Chimera ENCC 3000 2814 1 Biochemistry. 2002 Apr 2;41(13):4202-8  
Ethylene responsive element binding factor-2 3001 2815 1 Biochemistry. 2002 Apr 2;41(13):4202-8  
CRT/DRE binding factor 1 3002 2816 1 Biochemistry. 2002 Apr 2;41(13):4202-8  
Ethylene responsive element binding factor-2 3003-3007 2817-2821 5 Biochemistry. 2002 Apr 2;41(13):4202-8  
Chimera CNEC 3008 2822 1 Biochemistry. 2002 Apr 2;41(13):4202-8  
Chimera ENCC 3009 2823 1 Biochemistry. 2002 Apr 2;41(13):4202-8  
MAT alpha2/a1 complex 3010-3011 2824-2825 2 Structure (Camb). 2002 Jul;10(7):961-71  
MAT alpha2 3012-3013 2826-2827 2 Structure (Camb). 2002 Jul;10(7):961-71  
RNA polymerase sigma-54 factor 3014-3029 2828-2843 16 Nucleic Acids Res. 2002 Sep 15;30(18):4094-101  
DNA polymerase beta 3030-3037 2844-2851 8 Biochemistry. 2002 Sep 17;41(37):11226-35  
DNA polymerase beta 3038-3065 2852-2879 28 J Biol Chem. 2002 Sep 20;277(38):35550-60  
cAMP response element binding protein 3066-3070 2880-2884 5 Nucleic Acids Res. 2002 Mar 1;30(5):1240-6  
Vnd/NK-2 protein 3071-3095 2885-2909 25 Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12721-6  
Uracil DNA glycosylase 3096-3107 2910-2921 12 Biochemistry. 2002 Sep 17;41(37):11236-47  
cAMP receptor protein 3108-3109 2922-2923 2 J Biol Chem. 1998 Jan 9;273(2):705-12  
Flap endonuclease-1 3110-3119 2924-2933 10 J Biol Chem. 2002 Oct 4;277(40):37840-7  
DNA polymerase beta 3120-3131 2934-2945 12 Biochemistry. 1996 Jun 4;35(22):7041-50  
DNA polymerase I 3132-3186 2946-3000 55 J Biol Chem 2003 Feb 21;278(8):5694-701  
Tus protein 3187-3233 3001-3047 47 J Biol Chem 1997 Oct 17;272(42):26448-56  
Adenovirus proteinase 3234-3235 3048-3049 2 Biochemistry 2001 Nov 6;40(44):13237-45  
Precursor protein pVI 3236-3237 3050-3051 2 Biochemistry 2001 Nov 6;40(44):13237-45  
Adenovirus proteinase-Precorsor protein pVI compl 3238-3249 3052-3063 12 Biochemistry 2001 Nov 6;40(44):13237-45  
HMGB1 protein 3250 3064 1 Nucleic Acids Res 2000 Apr 1;28(7):1618-24  
HMGA1a protein 3251 3065 1 Nucleic Acids Res 2000 Apr 1;28(7):1618-24  
Hoxd1 protein 3252 3066 1 Cell Mol Neurobiol 2001 Aug;21(4):369-88  
Regulatory protein AreA 3253 3067 1 Biochim Biophys Acta 2003 May 30;1648(1-2):84-9  
Regulatory protein AreA 3254 3068 1 Biochim Biophys Acta 2000 Oct 2;1493(3):325-32  
Homeotic protein HAHB-4 3255 3069 1 Biochem J 1999 Jul 1;341 ( Pt 1):81-7  
Centromere-binding protein CBF1 3256-3257 3070-3071 2 J Biol Chem 1989 Jun 25;264(18):10843-50  
Tus protein 3258-3260 3072-3074 3 J Biol Chem 1992 Apr 15;267(11):7434-43  
Sox2 protein 3261-3267 3075-3081 7 J Biol Chem 2001 Dec 14;276(50):47296-302  
Centromere-binding protein CBF1 3268-3299 3082-3113 32 Nucleic Acids Res 2001 Mar 1;29(5):1054-60  
Cdc13 protein 3300-3302 3114-3116 3 Nucleic Acids Res 2002 Oct 1;30(19):4305-13  
Cdc13 protein 3303-3312 3117-3126 10 Science 1996 Oct 11;274(5285):249-52  
Myocyte enhancer factor-2C 3313-3327 3127-3141 15 Nucleic Acids Res 1997 Nov 15;25(22):4537-44  
Cdc13 protein 3328-3338 3142-3152 11 Proc Natl Acad Sci U S A 2000 Jun 6;97(12):6457-62  
Cdc13 protein 3339-3358 3153-3172 20 J Biol Chem 2001 Jul 6;276(27):24588-93  
HMGB1 protein 3359-3390 3173-3204 32 Biochemistry. 2000 Jul 25;39(29):8426-38  
Transcription factor Sp1 3391-3417 3205-3231 27 Biochemistry. 1998 May 12;37(19):6824-32  
Transcription factor 1 3418-3423 3232-3237 6 Biochemistry. 2002 Jun 18;41(24):7597-603  
UvrC protein 3424-3427 3238-3241 4 EMBO J. 2002 Nov 15;21(22):6257-66  
HMGB1 protein 3428-3438 3242-3252 11 Biochemistry. 1997 Sep 23;36(38):11428-36  
HU protein 3439-3448 3253-3262 10 Biochemistry. 2001 Feb 27;40(8):2588-98  
GCN4 protein 3449-3454 3263-3268 6 Protein Sci. 2002 Nov;11(11):2740-7  
Replication protein A 3455-3474 3269-3288 20 Biochemistry. 1999 Mar 30;38(13):3974-84  
Zif268 zinc finger protein 3475-3485 3289-3299 11 J Biol Chem 1999 Jul 2;274(27):19281-5  
HMGB1 protein 3486-3500 3300-3314 15 Biochemistry 2001 Aug 28;40(34):10254-61  
MutY glycosylase 3501-3516 3315-3330 16 Nucleic Acids Res. 2003 Jun 15;31(12):3038-49  
HMG-D protein 3517-3549 3331-3363 33 Nucleic Acids Res. 2003 Jun 1;31(11):2852-64  
I-PpoI endonuclease 3550-3551 3364-3365 2 J Mol Biol. 2000 Jul 21;300(4):877-87  
I-CreI endonuclease 3552-3558 3366-3372 7 Nucleic Acids Res. 2002 Sep 1;30(17):3870-9  
I-SceI endonuclease 3559 3373 1 J Biol Chem. 2001 Jul 6;276(27):25243-53  
GATA-1 protein 3560-3562 3374-3376 3 FEBS Lett. 1999 Feb 5;444(1):47-53  
H-NS protein 3563-3564 3377-3378 2 FEBS Lett. 1995 Feb 27;360(2):125-31  
Formamidopyrimidine-glycosylase 3565-3568 3379-3382 4 J Mol Biol. 2003 May 16;328(5):1047-60  
HU protein 3569-3572 3383-3386 4 J Biol Chem. 1995 Apr 28;270(17):10291-6  
PU.1 protein 3573-3598 3387-3412 26 J Mol Biol. 2003 May 9;328(4):805-19  
Adr1 protein 3599-3618 3413-3432 20 J Mol Biol. 2003 Jun 20;329(5):931-9  
Translin 3619 3433 1 Biochemistry. 2001 Nov 20;40(46):14081-8  
HMGB1 protein 3620-3627 3434-3441 8 Biochemistry. 2003 Mar 11;42(9):2664-71 PMID: 12614161  
EcoRV endonuclease 3628-3673 3442-3487 46 J Mol Biol. 2003 Aug 29; 331(5): 1005-16 PMID: 12927537  
cAMP receptor protein 3674-3703 3488-3517 30 Biochemistry. 2003 May 6; 42(17): 4809-18 PMID: 12718521  
cAMP receptor protein 3704-3719 3518-3533 16 Biochemistry. 1998 Apr 14;37(15):5194-200 PMID: 9548750  
cAMP receptor protein 3720-3735 3534-3549 16 Biochemistry. 1996 Jan 30;35(4):1162-72 PMID: 8573570  
cAMP receptor protein 3736-3747 3550-3561 12 Biochemistry. 2002 Dec 17;41(50):14935-43 PMID: 12475242  
CbpB protein 3748 3562 1 J Biol Chem. 1999 Nov 12; 274(46): 33105-13 PMID: 10551881  
DnaA protein 3749 3563 1 J Biol Chem. 1999 Nov 12; 274(46): 33105-13 PMID: 10551881  
Fis protein 3750 3564 1 J Biol Chem. 1999 Nov 12; 274(46): 33105-13 PMID: 10551881  
Integration host factor 3751 3565 1 J Biol Chem. 1999 Nov 12; 274(46): 33105-13 PMID: 10551881  
Lrp protein 3752 3566 1 J Biol Chem. 1999 Nov 12; 274(46): 33105-13 PMID: 10551881  
CbpA protein 3753-3754 3567-3568 2 J Biol Chem. 1999 Nov 12; 274(46): 33105-13 PMID: 10551881  
Dps protein 3755-3756 3569-3570 2 J Biol Chem. 1999 Nov 12; 274(46): 33105-13 PMID: 10551881  
Hfq protein 3757-3758 3571-3572 2 J Biol Chem. 1999 Nov 12; 274(46): 33105-13 PMID: 10551881  
H-NS protein 3759-3760 3573-3574 2 J Biol Chem. 1999 Nov 12; 274(46): 33105-13 PMID: 10551881  
HU protein 3761-3762 3575-3576 2 J Biol Chem. 1999 Nov 12; 274(46): 33105-13 PMID: 10551881  
IciA protein 3763-3764 3577-3578 2 J Biol Chem. 1999 Nov 12; 274(46): 33105-13 PMID: 10551881  
StpA protein 3765-3766 3579-3580 2 J Biol Chem. 1999 Nov 12; 274(46): 33105-13 PMID: 10551881  
EBNA1 nuclear protein 3767-3771 3581-3585 5 J Biol Chem. 2000 Jul 21;275(29):22273-7 PMID: 10801810  
SelB protein 3772-3785 3586-3599 14 J Mol Biol. 2002 Nov 15;324(1):137-50 PMID: 12421564  
Coat protein 3786-3827 3600-3641 42 Arch Biochem Biophys. 2002 Sep 1;405(1):122-9 PMID: 12176065  
Coat protein 3828-3842 3642-3656 15 J Biol Chem. 1996 Dec 13;271(50):31839-45 PMID: 8943226  
U1A protein 3843-3885 3657-3699 43 Nucleic Acids Res. 2002 Jan 15; 30(2): 550-8 PMID: 11788718  
U1A protein 3886-3908 3700-3722 23 J Biol Chem. 2002 Sep 6; 277(36): 33267-74 PMID: 12082087  
U1A protein 3909-3922 3723-3736 14 J Biol Chem. 2001 Jun 15;276(24):21476-81 PMID: 11297556  
PU.1 protein 3923-3973 3737-3787 51 J Mol Biol. 2004 Jan 2;335(1):113-27 PMID: 14659744  
TATA binding protein 3974-3983 3788-3797 10 J Biol Chem. 2001 Nov 23;276(47):43589-96 PMID: 11568187  
Cdc13 protein 3984-4002 3798-3816 19 Biochemistry. 2003 Apr 8; 42(13): 3751-8 PMID: 12667066  
EcoRV endonuclease 4003-4058 3817-3872 56 Biochemistry. 1995 Sep 5; 34(35): 11191-7 PMID: 7669777  
DnaA protein 4059-4076 3873-3890 18 J Biol Chem. 1995 Jul 21; 270(29): 17622-6 PMID: 7615570  
HMG-D protein 4077-4101 3891-3915 25 J Mol Biol. 2003 Aug 22;331(4):795-813 PMID: 12909011  
O6-Alkylguanine-DNA Alkyltransferase 4102-4165 3916-3979 64 J Biol Chem. 2003 Mar 7;278(10):7973-80 PMID: 12496275  
O6-Alkylguanine-DNA Alkyltransferase 4166-4206 3980-4020 41 Biochemistry. 2003 Feb 4;42(4):980-90 PMID: 12549918  
Ribosomal protein L1 4207-4232 4021-4046 26 Eur J Biochem. 1998 Aug 15;256(1):97-105 PMID: 9746351  
Immunoglobulin IgG 4233-4290 4047-4104 58 Biochemistry. 2003 Jan 14;42(1):30-41  
Immunoglobulin IgG 4291-4320 4105-4134 30 Biochemistry. 1999 Jan 12;38(2):560-8  
Immunoglobulin IgG 4321-4326 4135-4140 6 Biochemistry. 2001 Mar 6;40(9):2911-22  
E2 protein 4327-4354 4141-4168 28 J Mol Biol. 1998 Mar 6;276(4):809-18  
EcoRI endonuclease 4355-4373 4169-4187 19 Science. 1990 Nov 9;250(4982):776-86  
cAMP receptor protein 4374-4421 4188-4235 48 Biochemistry. 2004 Apr 27;43(16):4662-9  
UvrB protein 4422-4431 4236-4245 10 Biochemistry. 2004 Apr 13;43(14):4206-11  
cAMP receptor protein 4432-4523 4246-4337 92 Biochemistry. 2004 Jul 20;43(28):8901-10  
Endonuclease MunI 4524-4562 4338-4376 39 Biochemistry. 2001 Dec 11;40(49):14960-7  
cAMP receptor protein 4563-4568 4377-4382 6 J Mol Biol. 2001 Nov 16;314(1):75-82  
GCN4 protein 4569-4576 4383-4390 8 Biophys J. 2003 Mar;84(3):1867-75  
ZAP1 protein 4577-4589 4391-4403 13 Biochemistry. 2003 Feb 4;42(4):1053-61  
TATA Binding protein 4590-4646 4404-4460 57 J Mol Biol. 2004 Feb 27;336(4):829-42  
GATA-1 protein 4647-4658 4461-4472 12 Biochem Biophys Res Commun. 2004 Apr 9;316(3):910-7  
HoxA9 protein 4659-4688 4473-4502 30 Genes Dev. 2003 Aug 15;17(16):2060-72  
cAMP receptor protein 4689-4702 4503-4516 14 FEBS Lett. 2004 Apr 9;563(1-3):55-8  
cI repressor 4703-4724 4517-4538 22 Nature. 1987 Apr 30-May 6;326(6116):886-8  
Cro repressor 4725-4734 4539-4548 10 Nature. 1987 Apr 30-May 6;326(6116):886-8  
cI repressor 4735-4738 4549-4552 4 Nature. 1987 Apr 30-May 6;326(6116):886-8  
DNA polymerase I 4739-4774 4553-4588 36 Nucleic Acids Res. 2003 Oct 1;31(19):5590-7  
RecA protein 4775-4779 4589-4593 5 J Biol Chem. 2001 Mar 30;276(13):9613-9  
EcoRV endonuclease 4780-4806 4594-4620 27 J Mol Biol. 1997 May 30;269(1):82-101  
Rsrl DNA methyltransferase 4807-4822 4621-4636 16 Nucleic Acids Res. 2000 Oct 15;28(20):3962-71  
DNA Polymerase I 4823-4850 4637-4664 28 J Biol Chem. 2001 Aug 10;276(32):30167-77  
Uracil-DNA glycosylase 4851-4864 4665-4678 14 Nucleic Acids Res. 2001 Sep 15;29(18):3857-63  
T4 DNA polymerase 4865-4871 4679-4685 7 J Biol Chem. 2003 Jul 11;278(28):25435-47  
MutY glycosylase 4872-4876 4686-4690 5 Nucleic Acids Res. 1999 Aug 1;27(15):3197-204  
Purine repressor 4877-4884 4691-4698 8 J Mol Biol. 1999 Aug 13;291(2):347-61