HorA Server Transitive Detail

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: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.289 --> Intermediate <-- 1.319 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1jz7a5) through the intermediate protein (d1twda_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1twda_ Copper homeostasis protein CutCCutC-​like (Pfam 03932)TIM beta/​alpha-​barrelα/β
Hit d1jz7a5 beta-​Galactosidase,​ domain 3(Trans)glycosidasesTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 1.289 --> Intermediate
DALI alignment (Z-score: 8.2 Raw score:868.70) query 1 mietpyylidkakltrnmeriahvreksgAKALLALkcFATWsvFDLMRD-YMDGTTS-- 57 ::::::: :::: :::::: ::::::: d1twda_ 1 -----------------------------ALLEICC--YSME-cALTAQQnGADRVELca 28 query 58 -------SSLF-EVRLGRERFGKETHAYSVA-------------yGDNEIDEVVS-HADK 95 :::: ::::::::::::::::::: :::::::::: :::: d1twda_ 29 apkegglTPSLgVLKSVRQRVTIPVHPIIRPrggdfcysdgefaaILEDVRTVRElGFPG 88 query 96 IIFNS--------ISQLERFADKAAGIARGLR-LNPQrlgEWDVPKV-ERVMD-RINGFM 144 ::::: ::::::::::::::::::: :::: ::::::: ::::: :::::: d1twda_ 89 LVTGVldvdgnvdMPRMEKIMAAAGPLAVTFHrAFDM---CANPLYTlNNLAElGIARVL 145 query 145 IHnncenkdfglfDRMLGEIEErFGALiARVDWVSLGGGIHFtgddypvdaFSARLRAFS 204 :: ::::::::: :::: :::::::::::::: ::::::::: d1twda_ 146 TS-----gqksdaLQGLSKIME-LIAH-RDAPIIMAGAGVRA--------eNLHHFLDAG 190 query 205 drygvqIYLEPGeaSITKsTTLE-VTVLdtlynknlaivdssieahmldlliyretakvl 263 :::::: :::: :::: :::: d1twda_ 191 -----vLEVHSS--AGAW-QASPmRYRN-------------------------------- 210 query 264 pnegshsymicgksclagdvfgefrfaeelkvgdrisfqDAAGYtmvkknwfngvkmpai 323 ::::: d1twda_ 211 ---------------------------------------YSRYI---------------- 215 query 324 aireldgsvrtvreftyadyeqsls 348 d1twda_ 216 ------vdgaavaemkgiierhqak 234 FAST alignment (Normalized score: 4.77 Raw score:1361.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFA--TWSVFDLMRD-YMDGTTS 57 :::::: :::::::::: ::::::: d1twda_ 1 -----------------------------ALLEIC-----CYSMECALTAQQNGADRVEL 26 query 58 ----------SSLFEVRLGRERFGKETHAYSVAY----------------GDNEIDEVVS 91 ::::::::::::::::::::: :::::::::: d1twda_ 27 CAAPKEGGLTPSLGVLKSVRQRVTIPVHPII---RPRGGDFCYSDGEFAAILEDVRTVRE 83 query 92 -HADKIIFN---------SISQLERFADKAAGIARGLRLNPQRLGEW---------DVPK 132 ::::::: ::::::::::::::::::: :::: d1twda_ 84 LGFPGLVT-GVLDVDGNVDMPRMEKIMAAAGPLAVTF----------HRAFDMCANPLYT 132 query 133 VERVMD-RINGFMIHNNCENKDFG--------LFDRMLGEIEERFGALIARV----DWVS 179 :::::: ::::::: ::::::::::: :::: d1twda_ 133 LNNLAELGIARVLT----------SGQKSDALQGLSKIMELIA---------HRDAPIIM 173 query 180 LGGGIHFTGDD--YPVDAFSARLRAFSDRYGVQ---IYLEPGEASITK----STTLEVTV 230 ::::: :::::::: ::::: :::::::: d1twda_ 174 AGAGV------RAENLHHFLD------------AGVLEVHS-------SAGAWQASPMRY 208 query 231 LDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFA 290 d1twda_ 209 ------------------------------------------------------------ 209 query 291 EELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS-- 348 d1twda_ 209 ----------------------------------------------------------RN 210 query 349 ------------------------ 349 d1twda_ 211 YSRYIVDGAAVAEMKGIIERHQAK 234 TMalign alignment (TM-score: 0.42 Raw score:146.57) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSS-- 58 ::::: ::: ::::::::::::::::::: d1twda_ 1 ----------------------------ALLEI-CCY--SMECALTAQQNGADRVELCAA 29 query 59 ------SLF--EVRLGRERFGKETHAYSVA-------------YGDNEIDEVVS-HADKI 96 ::: ::::::::::::::::::: ::::::::::: ::::: d1twda_ 30 PKEGGLTPSLGVLKSVRQRVTIPVHPIIRPRGGDFCYSDGEFAAILEDVRTVRELGFPGL 89 query 97 IFNS------IS--QLERFADKAAGIARGLRLNPQRLGEWD-VPKVERVMD-RINGFMIH 146 :::: :: ::::::::::::::::::::: :::: ::::::::: :::::::: d1twda_ 90 VTGVLDVDGNVDMPRMEKIMAAAGPLAVTFHRAFD--MCANPLYTLNNLAELGIARVLTS 147 query 147 -NNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSD 205 ::: : :::::::::: :::: :::::::::::::: :: ::::::::: d1twda_ 148 GQKS-D-----ALQGLSKIME-LIAH-RDAPIIMAGAGVRA----EN---LHHFLDAGV- 191 query 206 RYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPN 265 :::: :: : ::: ::::: :: d1twda_ 192 ----LEVH-SS-A-GAW-QASPM--------------RY--------------------- 208 query 266 EGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTM---------------- 309 :: :::::: d1twda_ 209 ----------RN--------------------------YSRYIVDGAAVAEMKGIIERHQ 232 query 310 --VKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1twda_ 233 AK--------------------------------------- 234 HHsearch alignment (Probability: 0.20 E-value:0.04) query 45 FDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYG-------------DNEIDEVVS 91 :::::::::::::::::::::::::::::::::::::: ::::::::: d1twda_ 24 VELCAAPKEGGLTPSLGVLKSVRQRVTIPVHPIIRPRGGDFCYSDGEFAAILEDVRTVRE 83 query 92 HADKIIF---------NSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRING 142 ::::::: :::::::::::::::::::: ::::::::::::::::::: d1twda_ 84 LGFPGLVTGVLDVDGNVDMPRMEKIMAAAGPLAVTF-----HRAFDMCANPLYTLNNLAE 138 query 143 FMI-HNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGI 184 ::: ::::::::::: :::::::::::::::::: ::::::: d1twda_ 139 LGIARVLTSGQKSDA-LQGLSKIMELIAHRDAPI--IMAGAGV 178
Intermediate <-- 1.319 --> Hit
DALI alignment (Z-score: 11.5 Raw score:1204.40) d1twda_ 1 ----------------ALLEICCY--------------SMECALTAQQNGADRVELCaap 30 :::::::: ::::::::::::::::::: d1jz7a5 1 evriengllllngkplLIRGVNRHehhplhgqvmdeqtMVQDILLMKQNNFNAVRCS--- 57 d1twda_ 31 kegGLTPSLGVLKSVRQRvTIPVHPIIRpRGGD-----------fcYSDGEFAAILEDVR 79 ::::::::::::::: ::::::::: :::: :::::::::::::: d1jz7a5 58 ---HYPNHPLWYTLCDRY-GLYVVDEAN-IETHgmvpmnrltddprWLPAMSERVTRMVQ 112 d1twda_ 80 TVRELG-FPGLVTGvldvdGNVD--MPRMEKIMAAAGPLAVTFhRAFDmcanplytLNNL 136 :::::: ::::::: :::: :::::::::::::::::: :::: :::: d1jz7a5 113 RDRNHPsVIIWSLG--nesGHGAnhDALYRWIKSVDPSRPVQY-EGGG-------aDTTA 162 d1twda_ 137 aelgIARVLTSgqksDALQGLS---------KIMELIAH-RDAPIIMA-GAGVR----AE 181 ::::::: ::::::: :::::::: :::::::: ::::: :: d1jz7a5 163 ----TDIICPM----YARVDEDqpfpavpkwSIKKWLSLpGETRPLILcEYAHAmgnsLG 214 d1twda_ 182 NLHHFLDAG-----VLEVHS-SAGAWQAsPMRYRN------------------YSRYIVD 217 ::::::::: :::::: ::::::: :::::: ::::::: d1jz7a5 215 GFAKYWQAFrqyprLQGGFVwDWVDQSL-IKYDENgnpwsayggdfgdtpndrQFCMNGL 273 d1twda_ 218 G-------AAVAEMKGIIErhqak 234 : ::::::::::: d1jz7a5 274 VfadrtphPALTEAKHQQQ----- 292 FAST alignment (Normalized score: 5.92 Raw score:1547.00) d1twda_ 1 ----------------ALLEICCY---------------SMECALTAQQNGADRVELCAA 29 ::::::: ::::::::::::::::: d1jz7a5 1 EVRIENGLLLLNGKPLLIRGVNR-HEHHPLHGQVMDEQTMVQDILLMKQNNFNAVR---- 55 d1twda_ 30 PKEG--GLTPSLGVLKSVRQRVTIPVHPIIRPRGGDFC---------------YSDGEFA 72 :::::::::::::: :::::::: ::::::: d1jz7a5 56 ----CSHYPNHPLWYTLCDR-YGLYVVDE---------ANIETHGMVPMNRLTDDPRWLP 101 d1twda_ 73 AILEDVRTVRELG-------FPGLVTGVLDVDGNV-------DMPRMEKIMAA----AGP 114 ::::::::::: :::: ::::::::::: ::: d1jz7a5 102 AMSERVTRMVQ--RDRNHPSVIIW-----------SLGNESGHGANHDALYRWIKSVDPS 148 d1twda_ 115 LAVTFHRAFDMCANPLYTLNNLAEL---------GIARVLTSGQKSDALQGLS------- 158 :::: ::::::: d1jz7a5 149 RPVQ---------------------YEGGGADTTATDIICP------------MYARVDE 175 d1twda_ 159 ----------KIMELIAHRD-APIIMAGAGVR---------AENLHHFLDAG-------V 191 :::::::::: ::::::: ::::::::: : d1jz7a5 176 DQPFPAVPKWSIKKWLSLPGETRPLILC----EYAHAMGNSLGGFAKYWQ--AFRQYPRL 229 d1twda_ 192 LEVH-SSAGAWQASPMRYRNYSRYIVDGAAV----------------------------- 221 :::: :::::::::::: d1jz7a5 230 QGGFVWDWVDQSLIKYD--------------ENGNPWSAYGGDFGDTPNDRQFCMNGLVF 275 d1twda_ 222 -----AEMKGIIERHQAK-- 234 :::::::::: d1jz7a5 276 ADRTPHPALTEAKHQ---QQ 292 TMalign alignment (TM-score: 0.67 Raw score:156.68) d1twda_ 1 ----------------ALLEICCYS-------------M-ECALTAQQNGADRVELCAAP 30 ::::::::: : ::::::::::::::::: d1jz7a5 1 EVRIENGLLLLNGKPLLIRGVNRHEHHPLHGQVMDEQTMVQDILLMKQNNFNAVRCS--- 57 d1twda_ 31 KEGGLTPSLGVLKSVRQRVTIPVHPIIRPRGG----DF--C----YSDGEFAAILEDVRT 80 :::::::::: :::::::::::::::::: :: : ::::::::::::::: d1jz7a5 58 ---HYPNHPLWYT-LCDRYGLYVVDEANIETHGMVPMNRLTDDPRWLPAMSERVTRMVQR 113 d1twda_ 81 VRELGFPGLVTGVL-DVDGNV-DMPRMEKIMAAAGPLAVTFHRAFDMCANPLYTLNNLAE 138 :::::::::::::: ::::: ::::::::::::::::::: :: :: :: : :: d1jz7a5 114 DRNHPSVIIWSLGNE-SGHGANHDALYRWIKSVDPSRPVQY-EG--GG--AD-T--TA-- 162 d1twda_ 139 LGIARVLTSGQKSDALQGLS--------K-IMELIAH--RDAPIIMAGAGVR----AENL 183 : : ::::: ::::::: : ::::::: ::::::::::::: :::: d1jz7a5 163 T-D-IICPM----YARVDEDQPFPAVPKWSIKKWLSLPGETRPLILCEYAHAMGNSLGGF 216 d1twda_ 184 HHFLDAG-----VLEVHS-SAGAWQASPM---RYR--NYS-------------RY-IVD- 217 ::::::: :::::: :::::::::: ::: :: :: ::: d1jz7a5 217 AKYWQAFRQYPRLQGGFVWDWVDQSLIKYDENGNPWS-AYGGDFGDTPNDRQFCMNGLVF 275 d1twda_ 218 ----G-AAVAEMKGIIERHQAK 234 : ::::::::::: d1jz7a5 276 ADRTPHPALTEAKHQQQ----- 292 HHsearch alignment (Probability: 0.13 E-value:0.01) d1twda_ 12 CALTAQQNGADRVELCAAPKEGGLTPSLGVLKSVRQRVTIPVHPIIR--------PRGGD 63 ::::::::::::::::: ::::::::::::: ::: ::::: ::::: d1jz7a5 42 DILLMKQNNFNAVRCSH------YPNHPLWYTLCDR-YGL--YVVDEANIETHGMVPMNR 92 d1twda_ 64 FCYSDGEFAAILEDVRTVRELG--FPGLVTGVLDVDGN--VDMPRMEKIMAAAGP 114 :::::::::::::::::::::: :::::::::::::: ::::::::::::::: d1jz7a5 93 LTDDPRWLPAMSERVTRMVQRDRNHPSVIIWSLGNESGHGANHDALYRWIKSVDP 147