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 | d1d3ya_ | DNA topoisomerase IV, alpha subunit | DNA topoisomerase IV, alpha subunit | DNA topoisomerase IV, alpha subunit | 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 <-- 0.937 --> HitDALI alignment (Z-score: 5.4 Raw score:429.70) d1t6t1_ 1 ------------------------------------------------------------ 1 d1d3ya_ 1 qakifaqttkmlefakqlletddfstlreayyvsknwgearfddqqasnnviedleaalg 60 d1t6t1_ 1 -------------------------------------------prnlsewikelkkasRE 17 :: d1d3ya_ 61 vlrehlgfipeedgssvvgplkiieetpegelvvdctklgtgaynipndvtklnletdAD 120 d1t6t1_ 18 AVILVEGKNDKKALSKFSIK-----NVIDLS----gKRYADVVDMLEGKWEKVILLFDLD 68 :::::::::::::::::::: :::::: :::::::::::::::::::::::: d1d3ya_ 121 FILAIETSGMFARLNAERFWdkhncILVSLKgvparATRRFIKRLHEEHDLPVLVFTDGD 180 d1t6t1_ 69 THGE-RINQKMK---ELLSsqgfLVDEnFRNFlKKWN----------------------- 101 :::: ::::::: :::: :::: :::: :::: d1d3ya_ 181 PYGYlNIYRTLKvdkLSIP----AARL-IGVT-PQDIidydlpthplkeqdikrikdglk 234 d1t6t1_ 102 -----------------------iIHIEEI------------------------- 108 :::::: d1d3ya_ 235 nddfvrsfpewqkalkqmldmgvrAEQQSLakyglkyvvntylpekikdestwlp 289 FAST alignment (Normalized score: 4.19 Raw score:740.40) d1t6t1_ 1 PRNLSEWIKELKKAS--------------------------------------------- 15 d1d3ya_ 1 ---------------QAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQ 45 d1t6t1_ 16 ------------------------------------------------------------ 16 d1d3ya_ 46 QASNNVIEDLEAALGVLREHLGFIPEEDGSSVVGPLKIIEETPEGELVVDCTKLGTGAYN 105 d1t6t1_ 16 -------------REAVILVEGKNDKKALSKFSI------KNVIDLSGK--------RYA 48 :::::::::::::::::::: ::::: ::: d1d3ya_ 106 IPNDVTKLNLETDADFILAIETSGMFARLNAER-FWDKHNCILVS----LKGVPARATRR 160 d1t6t1_ 49 DVVDMLEGKW--EKVILLFDLDTHG-ERINQKMKELLSSQG------FLVDENF---RNF 96 :::::::: ::::::::::::: :::::::: ::::: ::: d1d3ya_ 161 FIKRLHEE--HDLPVLVFTDGDPYGYLNIYRTLK-------VDKLSIPAARL--IGVTPQ 209 d1t6t1_ 97 LKKWNI-----------------------------------------------IHIEEI- 108 :: :::: d1d3ya_ 210 DI----IDYDLPTHPLKEQDIKRIKDGLKNDDFVRSFPEWQKALKQMLDMGVRAEQQ--S 263 d1t6t1_ 109 -------------------------- 109 d1d3ya_ 264 LAKYGLKYVVNTYLPEKIKDESTWLP 289 TMalign alignment (TM-score: 0.61 Raw score:66.27) d1t6t1_ 1 ------------------------------------------------------------ 1 d1d3ya_ 1 QAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEAALG 60 d1t6t1_ 1 ----------------------------------------------------------PR 2 d1d3ya_ 61 VLREHLGFIPEEDGSSVVGPLKIIEETPEGELVVDCTKLGTGAYNIPNDVTKLNLETD-- 118 d1t6t1_ 3 NLSEWIKELKKASREAVILVEGKNDKKALSKFSIK-----NVIDLS--GKR--YADVVDM 53 :::::::::::::::::::::: :::::: ::: ::::::: d1d3ya_ 119 -------------ADFILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRL 165 d1t6t1_ 54 LEGKWEKVILLFDLDTHGE-RINQKMKE---LLSSQGFLVDENFR-N-FLKK-WNI---- 102 ::::::::::::::::::: :::::::: ::: :::: :: : :::: ::: d1d3ya_ 166 HEEHDLPVLVFTDGDPYGYLNIYRTLKVDKLSIP----AARL-IGVTPQDIIDYDLPTHP 220 d1t6t1_ 103 --------------------------------------IHIEEI---------------- 108 :::::: d1d3ya_ 221 LKEQDIKRIKDGLKNDDFVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEK 280 d1t6t1_ 109 --------- 109 d1d3ya_ 281 IKDESTWLP 289 HHsearch alignment (Probability: 0.30 E-value:0.03) d1t6t1_ 14 ASREAVILVEGKNDKKALSKFSIKN---VIDLSGKRYADVVD-----MLE-GKWEKVILL 64 ::::::::::::::::::::::::: :::::::::::::: ::: ::::::::: d1d3ya_ 117 TDADFILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRLHEEHDLPVLVF 176 d1t6t1_ 65 FDLDTHGERINQ 76 :::::::::::: d1d3ya_ 177 TDGDPYGYLNIY 188