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 <-- 1.749 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1itxa1) 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 d1itxa1 Chitinase A1(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 <-- 1.749 --> Hit
DALI alignment (Z-score: 11.8 Raw score:1290.30) d1twda_ 1 -----------ALLEICCY---------SMECaLTAQqnGADRVELcaapkegGLTP--- 37 :::::::: :::: :::: ::::::: :::: d1itxa1 1 lqpataeaadsYKIVGYYPswaaygrnyNVAD-IDPT--KVTHINY-------AFADicw 50 d1twda_ 38 -------------------------------------------------------slGVL 42 ::: d1itxa1 51 ngihgnpdpsgpnpvtwtcqneksqtinvpngtivlgdpwidtgktfagdtwdqpiaGNI 110 d1twda_ 43 KSVRQRV----TIPVHPIIR--pRGGDFCY---SDGEFAAILEDVRTVRE-LGFPGLVTG 92 ::::::: ::::::::: ::::::: ::::::::::::::::: ::::::::: d1itxa1 111 NQLNKLKqtnpNLKTIISVGgwtWSNRFSDvaaTAATREVFANSAVDFLRkYNFDGVDLD 170 d1twda_ 93 ------------vlDVDGNV-DMPRMEKIMAAAG--------PLAVTFHRafdmcaNPLY 131 :::::: ::::::::::::: :::::::: :::: d1itxa1 171 weypvsggldgnskRPEDKQnYTLLLSKIREKLDaagavdgkKYLLTIAS--gasaTYAA 228 d1twda_ 132 --TLNNLAELgIARVLTSGQK-----------SDAL-----------------QGLSKIM 161 :::::::: :::::::::: :::: ::::::: d1itxa1 229 ntELAKIAAI-VDWINIMTYDfngawqkisahNAPLnydpaasaagvpdantfNVAAGAQ 287 d1twda_ 162 ELIAHRDA-pIIMAGAG-----vRAENLHHFLDAGVLEVHS-SAGAwqaspmryrnysry 214 :::::::: ::::::: :::::::::::::::::: :::: d1itxa1 288 GHLDAGVPaaKLVLGVPfddaesVGYKTAYIKSKGLGGAMFwELSG-------------- 333 d1twda_ 215 iVDGAAVAEMKGIIerhqak 234 ::::::::::::: d1itxa1 334 dRNKTLQNKLKADL------ 347 FAST alignment (Normalized score: 6.06 Raw score:1727.00) d1twda_ 1 -----------ALLEICCYSME----------CALTAQQN----GADRVELCAAPKEGGL 35 ::::::: :::: ::::::: d1itxa1 1 LQPATAEAADSYKIVGYY----PSWAAYGRNYNVAD----IDPTKVTHINY--------- 43 d1twda_ 36 TPSL-------------------------------------------------------- 39 d1itxa1 44 ----AFADICWNGIHGNPDPSGPNPVTWTCQNEKSQTINVPNGTIVLGDPWIDTGKTFAG 99 d1twda_ 40 --------GVLKSVR---QRVT-IPVHPIIRPRGGDFC--------------YSDGEFAA 73 ::::::: :::: :::::: :::::::: d1itxa1 100 DTWDQPIAGNINQLNKLKQTNPNLKTIIS---------VGGWTWSNRFSDVAATAATREV 150 d1twda_ 74 ILEDVRTV-RELGFPGLVTGVLDVDGNV--------------------DMPRMEKIMAAA 112 :::::::: :::::::::::: ::::::::::: d1itxa1 151 FANSAVDFLRKYNFDGVDLDW-------EYPVSGGLDGNSKRPEDKQNYTLLLSKIREK- 202 d1twda_ 113 G----------PLAVTFHRAFDMC-----------ANPLYTLNNLAELGIARVLTSGQKS 151 :::::: :::::::: :::::::: d1itxa1 203 -LDAAGAVDGKKYLLTI-------ASGASATYAANTELAKIAA-----IVDWINIM---- 245 d1twda_ 152 DALQ------------------------------------GLSKIMELIAHRDAP----- 170 ::::::::::: d1itxa1 246 ----TYDFNGAWQKISAHNAPLNYDPAASAAGVPDANTFNVAAGAQGHLDA----GVPAA 297 d1twda_ 171 IIMAGAG----VRAE----NLHHFLDAGVLEVHSSAGAWQASPMRYRNYSRYI------V 216 :::: :::: ::::::::::::::: : d1itxa1 298 KLVL---GVPFDDAESVGYKTAYIKSKGLGGAMF-------------------WELSGDR 335 d1twda_ 217 DGAAVAEMKGIIERHQAK-- 234 :::::::::: d1itxa1 336 NKTLQNKLKA--------DL 347 TMalign alignment (TM-score: 0.69 Raw score:161.23) d1twda_ 1 -----------ALLEICCYS--M----ECALTAQQNGADRVELCAA-------------- 29 ::::::::: : ::::::::::::::::::: d1itxa1 1 LQPATAEAADSYKIVGYYPSWAAYGRNYNVADIDPTKVTHINYAFADICWNGIHGNPDPS 60 d1twda_ 30 PKE---------------------GGLTP-S--LG--------------VLKSVRQRVT- 50 ::: ::: : :: :::::::::: d1itxa1 61 GPNPVTWTCQNEKSQTINVPNGTI--VLGDPWIDTGKTFAGDTWDQPIAGNINQLNKLKQ 118 d1twda_ 51 ----IPVHPIIRP-RGGD-FCYS--D-GEFAAILEDVRTVREL-GFPGLVTGV--LD--- 95 ::::::::: :::: :::: : :::::::::::::::: ::::::::: :: d1itxa1 119 TNPNLKTIISVGGWTWSNRFSDVAATAATREVFANSAVDFLRKYNFDGVDLDWEYPVSGG 178 d1twda_ 96 ------VD-GNVD-MPRMEKIMAAAG--------PLAVTFHRAFD-MCANPLYTLNNLAE 138 :: :::: :::::::::::: ::::::::::: ::::: :::::::: d1itxa1 179 LDGNSKRPEDKQNYTLLLSKIREKLDAAGAVDGKKYLLTIASGASATYAAN-TELAKIAA 237 d1twda_ 139 LGIARVLTSGQKS----------DAL-----------------QGLSK-IMELIA-HRDA 169 :::::::::::: ::: ::::: :::::: :::: d1itxa1 238 -IVDWINIMTYDFNGAWQKISAHNAPLNYDPAASAAGVPDANTFNVAAGAQGHLDAGVPA 296 d1twda_ 170 PIIMAGAGVRAE-NLHHFLDAG----VLEVHSSAGAWQASPMRYRNYSRYIVDGAAVAEM 224 :::::::::::: ::::::::: ::::::::: ::::: ::: d1itxa1 297 AKLVLGVPFDDAESVGYKTAYIKSKGLGGAMFWEL---------------SGDRN--KTL 339 d1twda_ 225 KGIIERHQAK 234 :::::::: d1itxa1 340 QNKLKADL-- 347 HHsearch alignment (Probability: 0.27 E-value:0.02) d1twda_ 51 IPVHPIIRPRGGD----F---CYSDGEFAA-ILEDVRTVRELGFPGLVTGVLDV 96 ::::::::::::: : ::::::::: ::::::::::::::::::::::: d1itxa1 121 PNLKTIISVGGWTWSNRFSDVAATAATREVFANSAVDFLRKYNFDGVDLDWEYP 174