Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets.
J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu
Query: T592_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1t6t1_ | Hypothetical protein aq 2086 | Toprim domain (Pfam 01751) | Toprim domain (Pfam 01751) | α/β |
| Hit | d1gkub3 | Topoisomerase (domain( of reverse gyrase | Prokaryotic type I DNA topoisomerase | Prokaryotic type I DNA topoisomerase | multi |
Query <-- 0.610 --> IntermediateDALI alignment (Z-score: 4.8 Raw score:306.10) query 1 npneayrhymkklsyetDIADLSIDikkgyEGIIVVDvRDAEaYKECH----IPTAISIP 56 :::::::: ::::::: :::: ::::: :::::::: d1t6t1_ 1 -----------prnlseWIKELKKA----sREAVILV-EGKN-DKKALskfsIKNVIDLS 43 query 57 gnKINEdTTKRLSKEK-VIITYCWGPA--CNGATKAAAKFAQLGFRVKE------liggi 107 :::: ::::::::: :::::::::: :::::::::::::::::::: d1t6t1_ 44 gkRYAD-VVDMLEGKWeKVILLFDLDThgERINQKMKELLSSQGFLVDEnfrnflkkwni 102 query 108 EYWRkengevegtlgakadlfwnmkkesle 137 :::: d1t6t1_ 103 IHIE------------------------ei 108 FAST alignment (Normalized score: 4.56 Raw score:554.40) query 1 NPNEAYRHYMKKLSYET------DIADLSIDIKKGYEGIIVVDVRDAEAYKECH------ 48 ::::::::: ::::::: ::::::: d1t6t1_ 1 -----------------PRNLSEWIKELKKAS----REAVILV-EGKNDKK---ALSKFS 35 query 49 IPTAISIPGNKI-----NEDTTKRLSKE--KVIITYCWGPA---CNGATKAAAKFAQLGF 98 :::::: ::::::: ::: :::::::::: :::::::::::::::: d1t6t1_ 36 IKNVID------LSGKRYADVVDM-LEGKWEKVILLFDLD-THGERINQKMKELLSSQGF 87 query 99 RVKELIGGIEYWRKENGEVEGTLGAKADLFWNMKKESLE------------------ 137 ::: d1t6t1_ 88 LVD------------------------------------ENFRNFLKKWNIIHIEEI 108 TMalign alignment (TM-score: 0.48 Raw score:65.09) query 1 --NPNEAYRHYMKKLSYETDIA-DLS-IDIKKGYEGIIVVDVRDAEAYKECHI--P---- 50 :: ::: ::: :::::::::: : :: ::: : d1t6t1_ 1 PR------------------NLSEWIKELK-KASREAVILV-E----GK-NDKKALSKFS 35 query 51 -T-AISIPGNKINEDTTKRL--SKEKVIITYCWGPA--CNGATKAAAKFAQLGFRVKE-- 102 : :::::::::: :::::: ::: :::::::::: :::::::::::::::::::: d1t6t1_ 36 IKNVIDLSGKRYA-DVVDMLEGKWE-KVILLFDLDTHGERINQKMKELLSSQGFLVDENF 93 query 103 LI-GG---IEYWRKENGEVEGTLGAKADLFWNMKKESLE 137 :: :: :::::: : d1t6t1_ 94 RNFLKKWNIIHIEE--I---------------------- 108 HHsearch alignment (Probability: 0.05 E-value:0.04) query 49 IPTAISIPGNKINEDTTKRLSKEKVIITYCWGPACNGATKAAA----KFAQLGFRV 100 ::::::::::::::::::::::::::::::::: :::::::: ::::::::: d1t6t1_ 36 IKNVIDLSGKRYADVVDMLEGKWEKVILLFDLD--THGERINQKMKELLSSQGFLV 89
Intermediate <-- 1.264 --> HitDALI alignment (Z-score: 6.7 Raw score:414.50) d1t6t1_ 1 prnlsewikelkkasREAVILVEGKNDKKALSKFS---------------------ikNV 39 :::::::::::::::::::: :: d1gkub3 1 ---------qefdliKPALFIVESPTKARQISRFFgkpsvkvldgavvyeipmqkyvlMV 51 d1t6t1_ 40 IDLS--------------------------------gkRYADVVDMLEgKWEKVILLFDL 67 :::: :::::::::: ::::::::::: d1gkub3 52 TASIghvvdlitnrgfhgvlvngrfvpvyasikdnsrsRIEALRKLAH-DAEFVIVGTDP 110 d1t6t1_ 68 DTHGERINQKMKELLSsQGFLVDEnfRNFLkkwniihIEEI------------------- 108 :::::::::::::::: ::::::: :::: :::: d1gkub3 111 DTEGEKIAWDLKNLLS-GCGAVKR--AEFH------eVTRRailealeslrdvdenlvka 161 d1t6t1_ 109 ------------------------------------------------------------ 109 d1gkub3 162 qvvrriedrwigfvlsqklwerfnnrnlsagraqtlvlgwiidrfqesrerrkiaivrdf 221 d1t6t1_ 109 ------------------------------------------------------------ 109 d1gkub3 222 dlvlehdeeefdltiklveereelrtplppyttetmlsdanrilkfsvkqtmqiaqelfe 281 d1t6t1_ 109 ------------------------------------------------------------ 109 d1gkub3 282 nglityhrtdstrvsdvgqriakeylgddfvgrewgesgahecirptrpltrddvqrliq 341 d1t6t1_ 109 ------------------------------------------------------------ 109 d1gkub3 342 egvlvveglrwehfalydlifrrfmasqcrpfkvvvkkysiefdgktaeeerivraegra 401 d1t6t1_ 109 ------------------------------------------------------------ 109 d1gkub3 402 yelyravwvknelptgtfrvkaevksvpkvlpftqseiiqmmkergigrpstyativdrl 461 d1t6t1_ 109 ------------------------------------------------------------ 109 d1gkub3 462 fmrnyvvekygrmiptklgidvfrflvrryakfvsedrtrdlesrmdaiergeldylkal 521 d1t6t1_ 109 ----------- 109 d1gkub3 522 edmyaeiksid 532 FAST alignment (Normalized score: 3.02 Raw score:723.90) d1t6t1_ 1 PRNLSEWIKELKKAS------REAVILVEGKNDKKALSKFSI------------------ 36 :::::::::::::::::: d1gkub3 1 ---------------QEFDLIKPALFIVESPTKARQISR---FFGKPSVKVLDGAVVYEI 42 d1t6t1_ 37 ------KNVIDLSGK------------------------------------RYADVVDML 54 ::::: ::::::::: d1gkub3 43 PMQKYVLMVTA----SIGHVVDLITNRGFHGVLVNGRFVPVYASIKDNSRSRIEALRKLA 98 d1t6t1_ 55 EGKWEKVILLFDLDTHGERINQKMKELLSSQGFLVDENFRNFLKKWNIIHIEEI------ 108 : :::::::::::::::::::::::::::: ::::: d1gkub3 99 H-DAEFVIVGTDPDTEGEKIAWDLKNLLSG-CGAVK------------------RAEFHE 138 d1t6t1_ 109 ------------------------------------------------------------ 109 d1gkub3 139 VTRRAILEALESLRDVDENLVKAQVVRRIEDRWIGFVLSQKLWERFNNRNLSAGRAQTLV 198 d1t6t1_ 109 ------------------------------------------------------------ 109 d1gkub3 199 LGWIIDRFQESRERRKIAIVRDFDLVLEHDEEEFDLTIKLVEEREELRTPLPPYTTETML 258 d1t6t1_ 109 ------------------------------------------------------------ 109 d1gkub3 259 SDANRILKFSVKQTMQIAQELFENGLITYHRTDSTRVSDVGQRIAKEYLGDDFVGREWGE 318 d1t6t1_ 109 ------------------------------------------------------------ 109 d1gkub3 319 SGAHECIRPTRPLTRDDVQRLIQEGVLVVEGLRWEHFALYDLIFRRFMASQCRPFKVVVK 378 d1t6t1_ 109 ------------------------------------------------------------ 109 d1gkub3 379 KYSIEFDGKTAEEERIVRAEGRAYELYRAVWVKNELPTGTFRVKAEVKSVPKVLPFTQSE 438 d1t6t1_ 109 ------------------------------------------------------------ 109 d1gkub3 439 IIQMMKERGIGRPSTYATIVDRLFMRNYVVEKYGRMIPTKLGIDVFRFLVRRYAKFVSED 498 d1t6t1_ 109 ---------------------------------- 109 d1gkub3 499 RTRDLESRMDAIERGELDYLKALEDMYAEIKSID 532 TMalign alignment (TM-score: 0.32 Raw score:34.08) d1t6t1_ 1 ------------------------------------------------------------ 1 d1gkub3 1 QEFDLIKPALFIVESPTKARQISRFFGKPSVKVLDGAVVYEIPMQKYVLMVTASIGHVVD 60 d1t6t1_ 1 ------------------------------------------------------------ 1 d1gkub3 61 LITNRGFHGVLVNGRFVPVYASIKDNSRSRIEALRKLAHDAEFVIVGTDPDTEGEKIAWD 120 d1t6t1_ 1 ------------------------------------------------------------ 1 d1gkub3 121 LKNLLSGCGAVKRAEFHEVTRRAILEALESLRDVDENLVKAQVVRRIEDRWIGFVLSQKL 180 d1t6t1_ 1 ------------------------------------------------------------ 1 d1gkub3 181 WERFNNRNLSAGRAQTLVLGWIIDRFQESRERRKIAIVRDFDLVLEHDEEEFDLTIKLVE 240 d1t6t1_ 1 ---------------PRNLSE-WI------K-ELKKASREAVI--LVEGKNDKKALSKFS 35 :::: :: : ::::::: :: :::: : :: :: d1gkub3 241 EREELRTPLPPYTTE--TMLSDANRILKFSVKQTMQIAQ--ELFENGLI--T--YH--RT 290 d1t6t1_ 36 -----------------------------------IKNVIDLSGKRYADVVDMLEGKWEK 60 d1gkub3 291 DSTRVSDVGQRIAKEYLGDDFVGREWGESGAHECI------------------------- 325 d1t6t1_ 61 VILLFDLDTHGER--IN-QKMKELLS-SQGFLVD--ENFRNFLKKWNII----------- 103 ::::: :: :: :::::::: :::::: :::::::::: :: d1gkub3 326 ---RPTRP---LTRDDVQRLIQEGVLV-VEGLRWEHFALYDLIFRR-FMASQCRPFKVVV 377 d1t6t1_ 104 ------------------------------------------------------------ 104 d1gkub3 378 KKYSIEFDGKTAEEERIVRAEGRAYELYRAVWVKNELPTGTFRVKAEVKSVPKVLPFTQS 437 d1t6t1_ 104 ------------------------------------------------------------ 104 d1gkub3 438 EIIQMMKERGIGRPSTYATIVDRLFMRNYVVEKYGRMIPTKLGIDVFRFLVRRYAKFVSE 497 d1t6t1_ 104 -----------------------------------HIEEI 108 d1gkub3 498 DRTRDLESRMDAIERGELDYLKALEDMYAEIKSID----- 532 HHsearch alignment (Probability: 0.88 E-value:0.00) d1t6t1_ 44 GKRYADVVDMLEGKWEKVILLFDLDTHGERINQKMKELLSSQ 85 :::::::::::::::::::::::::::::::::::::::::: d1gkub3 87 SRSRIEALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNLLSGC 128