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 | d1mw9x_ | DNA topoisomerase I, 67K N-terminal domain | 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 <-- 1.085 --> HitDALI alignment (Z-score: 7.0 Raw score:407.70) d1t6t1_ 1 prnlsewikelkkasrEAVILVEGKNDKKALSkFSIK---NVIDLS-------------- 43 :::::::::::::::: :::: :::::: d1mw9x_ 1 ---------------gKALVIVESPAKAKTIN-KYLGsdyVVKSSVghirdlptergalv 44 d1t6t1_ 44 ---------------------gKRYADVVDMLEgKWEKVILLFDLDTHGERINQKMKELL 82 ::::::::::: :::::::::::::::::::::::::: d1mw9x_ 45 nrmgvdpwhnweahyevlpgkeKVVSELKQLAE-KADHIYLATDLDREGEAIAWHLREVI 103 d1t6t1_ 83 sSQGF-LVDEnfRNFL-------------------------------------------- 97 :::: :::: :::: d1mw9x_ 104 -GGDDaRYSR--VVFNeitknairqafnkpgelnidrvnaqqarrfmdrvvgymvspllw 160 d1t6t1_ 98 ------------------------------------------------------------ 98 d1mw9x_ 161 kkiarglsagrvqsvavrlvverereikafvpeefwevdastttpsgealalqvthqndk 220 d1t6t1_ 98 ------------------------------------------------------------ 98 d1mw9x_ 221 pfrpvnkeqtqaavsllekarysvleredkpttskpgapfitstlqqaastrlgfgvkkt 280 d1t6t1_ 98 kkwniihIEEI------------------------------------------------- 108 :::: d1mw9x_ 281 mmmaqrlYEAGyitymrtdstnlsqdavnmvrgyisdnfgkkylpespnqyareairpsd 340 d1t6t1_ 109 ------------------------------------------------------------ 109 d1mw9x_ 341 vnvmaeslkdmeadaqklyqliwrqfvacqmtpakydsttltvgagdfrlkargrilrfd 400 d1t6t1_ 109 ------------------------------------------------------------ 109 d1mw9x_ 401 gwtkvmpaledrilpavnkgdaltlveltpaqhftkpparfseaslvkelekrgigrpst 460 d1t6t1_ 109 ------------------------------------------------------------ 109 d1mw9x_ 461 yasiistiqdrgyvrvenrrfyaekmgeivtdrleenfrelmnydftaqmennldqvanh 520 d1t6t1_ 109 ------------------------------------ 109 d1mw9x_ 521 eaewkavldhffsdftqqldkaekdpeeggmrpnqm 556 FAST alignment (Normalized score: 2.53 Raw score:620.20) d1t6t1_ 1 PRNLSEWIKELKKASR-EAVILVEGKNDKKALSKFSIK------NVIDLSGK-------- 45 ::::::::::::::::: :::: d1mw9x_ 1 ----------------GKALVIVESPAKAKTINK----YLGSDYVVKS----SVGHIRDL 36 d1t6t1_ 46 -------------------------------RYADVVDMLEGKWEKVILLFDLDTHGERI 74 :::::::: :::::::::::::::::::: d1mw9x_ 37 PTERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQL-AEKADHIYLATDLDREGEAI 95 d1t6t1_ 75 NQKMKELLSSQGFLVDENFRNFLKKWNIIHIEEI-------------------------- 108 ::::::: d1mw9x_ 96 AWHLREV---------------------------IGGDDARYSRVVFNEITKNAIRQAFN 128 d1t6t1_ 109 ------------------------------------------------------------ 109 d1mw9x_ 129 KPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIK 188 d1t6t1_ 109 ------------------------------------------------------------ 109 d1mw9x_ 189 AFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLERE 248 d1t6t1_ 109 ------------------------------------------------------------ 109 d1mw9x_ 249 DKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAV 308 d1t6t1_ 109 ------------------------------------------------------------ 109 d1mw9x_ 309 NMVRGYISDNFGKKYLPESPNQYAREAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVA 368 d1t6t1_ 109 ------------------------------------------------------------ 109 d1mw9x_ 369 CQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALEDRILPAVNKGDALTLVEL 428 d1t6t1_ 109 ------------------------------------------------------------ 109 d1mw9x_ 429 TPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGE 488 d1t6t1_ 109 ------------------------------------------------------------ 109 d1mw9x_ 489 IVTDRLEENFRELMNYDFTAQMENNLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEE 548 d1t6t1_ 109 -------- 109 d1mw9x_ 549 GGMRPNQM 556 TMalign alignment (TM-score: 0.31 Raw score:33.69) d1t6t1_ 1 ------------------------------------------------------------ 1 d1mw9x_ 1 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTERGALVNRMGVDPWHNWEAHYE 60 d1t6t1_ 1 ------------------------------------------------------------ 1 d1mw9x_ 61 VLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITK 120 d1t6t1_ 1 -----------------------------------------------P------------ 1 : d1mw9x_ 121 NAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLV 180 d1t6t1_ 2 ------------------------------------------------------------ 2 d1mw9x_ 181 VEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKA 240 d1t6t1_ 2 ------------------------------------------------------------ 2 d1mw9x_ 241 RYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDS 300 d1t6t1_ 2 ------------------------------------------------------------ 2 d1mw9x_ 301 TNLSQDAVNMVRGYISDNFGKKYLPESPNQYAREAIRPSDVNVMAESLKDMEADAQKLYQ 360 d1t6t1_ 2 ------------------------------------------------------------ 2 d1mw9x_ 361 LIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALEDRILPAVNKG 420 d1t6t1_ 2 ------------------------------------------RNLSEWIK-E-LK----- 12 ::::::: : :: d1mw9x_ 421 DALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYA-SIISTIQDRGYVRVENR 479 d1t6t1_ 13 ----K-ASREA-V-I---LVE--GKNDKKA------------------LSKFSIKNVIDL 42 : ::::: : : ::: ::::: : d1mw9x_ 480 RFYAEKMGEIVTDRLEENFRELMNYDFT-AQMENNLDQVANHEAEWKA------------ 526 d1t6t1_ 43 SGKRYADVVDMLEGKWEKVILLFDLDTHGERINQKMKELLSSQG----FLV---DENFRN 95 :::::::::::::::::::: ::: d1mw9x_ 527 ------------------------VLDHFFSDFTQQLDKAEKDPEEGGMRPNQM------ 556 d1t6t1_ 96 FLKKWNIIHIEEI 108 d1mw9x_ 557 ------------- 557 HHsearch alignment (Probability: 0.88 E-value:0.00) d1t6t1_ 43 SGKRYADVVDMLEGKWEKVILLFDLDTHGERINQKMKELLSSQG 86 :::::::::::::::::::::::::::::::::::::::::::: d1mw9x_ 64 GKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDD 107