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 <-- 2.347 --> Intermediate <-- 2.340 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1twda_) through the intermediate protein (d1tqja_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1tqja_ D-​ribulose-​5-​phosphate 3-​epimeraseRibulose-​phoshate binding barrelTIM beta/​alpha-​barrelα/β
Hit d1twda_ Copper homeostasis protein CutCCutC-​like (Pfam 03932)TIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 2.347 --> Intermediate
DALI alignment (Z-score: 13.0 Raw score:1145.60) query 1 mietpyylidkakltrnmeriahvreksGAKALLALKCF---aTWSVFDLMRD-YMDGTT 56 ::::::::::: :::::::::: :::::: d1tqja_ 1 ---------------------------kNIVVAPSILSAdfsrLGEEIKAVDEaGADWIH 33 query 57 SSS------------LFEVRLGRERFGKETHAYSV--AYGDnEIDEVVS-HADKIIFNS- 100 ::: :::::::::::::::::::: :::: ::::::: ::::::::: d1tqja_ 34 VDVmdgrfvpnitigPLIVDAIRPLTKKTLDVHLMivEPEK-YVEDFAKaGADIISVHVe 92 query 101 ---ISQLERFADKAA--GIARGLRLNPQrlgeWDVPKVERVMDRINGFMIHN-NCENkdf 154 :::::::::::: ::::::::::: :::::::::::::::::::: :::: d1tqja_ 93 hnaSPHLHRTLCQIRelGKKAGAVLNPS----TPLDFLEYVLPVCDLILIMSvNPQS--- 145 query 155 glFDRMLGEIEeRFGALIA---RVDWVSLGGGIHFtgddypvdaFSARLRAFSdrygvqI 211 ::::::::: ::::::: ::::::::::::: ::::::::: : d1tqja_ 146 -fIPEVLPKIR-ALRQMCDergLDPWIEVDGGLKP--------nNTWQVLEAG-----aN 190 query 212 YLEPGEASITKsttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsy 271 ::::::::::: d1tqja_ 191 AIVAGSAVFNA------------------------------------------------- 201 query 272 micgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgs 331 d1tqja_ 202 ------------------------------------------------------------ 202 query 332 vrtvreftyadyeqsls 348 d1tqja_ 202 --pnyaeaiagvrnskr 216 FAST alignment (Normalized score: 7.32 Raw score:2007.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS-GAKALLALK-CFA--TWSVFDLMRD-YMDGT 55 ::::::::: ::: :::::::::: ::::: d1tqja_ 1 ----------------------------KNIVVAPSILSADFSRLGEEIKAVDEAGADWI 32 query 56 TS------------SSLFEVRLGRERFGKETHAYSVAY----GDNEIDEVVS-HADKIIF 98 :: ::::::::::::::::::::: :::::::::: ::::::: d1tqja_ 33 HVDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHL---MIVEPEKYVEDFAKAGADIISV 89 query 99 N--SISQ---LERFADKA---AGIARGLRLNPQRLGE-WDVPKVERVMDRINGFMIHNNC 149 :::: ::::::: ::::::::::: :::::::::::::::::::: d1tqja_ 90 -HVEHNASPHLHRTLCQ-IRELGKKAGAVLNP-----STPLDFLEYVLPVCDLILIMS-- 140 query 150 ENKD------FGLFDRMLGEIEERFGALIARV----DWVSLGGGIHFTGDDYPVDA---F 196 ::::::::::::::::: ::::::::: : d1tqja_ 141 ----VNPQSFIPEVLPKIRALRQMCDE-----RGLDPWIEVDGGL-----------KPNN 180 query 197 SARLRAFSDRYGVQ---IYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDL 253 :::::: ::::::::: d1tqja_ 181 TWQVLE--------AGANAIVAGSAV---------------------------------- 198 query 254 LIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKN 313 d1tqja_ 199 ------------------------------------------------------------ 199 query 314 WFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS------------------ 348 d1tqja_ 199 -----------------------------------FNAPNYAEAIAGVRNSKR 216 TMalign alignment (TM-score: 0.43 Raw score:149.23) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF-A--TWSVFDLMRD-YMDGTT 56 :::::::::::: : :::::::::: :::::: d1tqja_ 1 ---------------------------KNIVVAPSILSADFSRLGEEIKAVDEAGADWIH 33 query 57 S-S-----------SLFEVRLGRERFGKETHAYSVA--YGDNEIDEVVS-HADKIIFNS- 100 : : :::::::::::::::::::::: ::: ::::::: ::::::::: d1tqja_ 34 VDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHLMIVEPEK-YVEDFAKAGADIISVHVE 92 query 101 ---ISQLERFADKAA--GIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNN--CENKD 153 :::::::::::: ::::::::::: :::: ::::::::::::::::: ::: d1tqja_ 93 HNASPHLHRTLCQIRELGKKAGAVLNPS---TPLD-FLEYVLPVCDLILIMSVNPQSF-- 146 query 154 FGLFDRMLGEIEERFGALIA---RVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQ 210 : ::::::::::::::: ::::::::::::: ::: :: :: ::: : d1tqja_ 147 ---I-PEVLPKIRALRQMCDERGLDPWIEVDGGLKP----NNT--WQ-VL-EAG-----A 189 query 211 IYLEPGEASITKST-------------TLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYR 257 :::::::::::::: d1tqja_ 190 NAIVAGSAVFNAPNYAEAIAGVRNSKR--------------------------------- 216 query 258 ETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNG 317 d1tqja_ 217 ------------------------------------------------------------ 217 query 318 VKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1tqja_ 217 ------------------------------- 217 HHsearch alignment (Probability: 0.21 E-value:0.01) query 75 HAYSVAYGDNEIDEVVSHADKIIFN--SISQLERFADKAAG--IARGLRLNPQRLGEWDV 130 ::::::::::::::::::::::::: :::::::::::::: :::::::::: ::: d1tqja_ 68 MIVEPEKYVEDFAKAGADIISVHVEHNASPHLHRTLCQIRELGKKAGAVLNPS----TPL 123 query 131 PKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDW-VSLG 181 ::::::::::::::::::::::::::::::::::::::::::::::: :::: d1tqja_ 124 DFLEYVLPVCDLILIMSVNPQSFIPEVLPKIRALRQMCDERGLDPWIEVDGG 175
Intermediate <-- 2.340 --> Hit
DALI alignment (Z-score: 14.9 Raw score:1342.80) d1tqja_ 1 knIVVAPSILsadfsrLGEEIKAVDEAGADWIHVDvmdgrfvPNIT--IGPLIVDAIRPL 58 :::::::: ::::::::::::::::::: :::: :::::::::::: d1twda_ 1 --ALLEICCY------SMECALTAQQNGADRVELC----aapKEGGltPSLGVLKSVRQR 48 d1tqja_ 59 TKKTLDVHLMIV------------EPEKYVEDFAKAGADIISVHVEH----nasPHLHRT 102 :::::::::::: ::::::::::::::::::::::: :::::: d1twda_ 49 VTIPVHPIIRPRggdfcysdgefaAILEDVRTVRELGFPGLVTGVLDvdgnvdmPRMEKI 108 d1tqja_ 103 LCQIreLGKKAGAV-LNPST--PLDFLEYVLP-VCDLILIMsvnpQSFIPeVLPKIRALR 158 :::: :::::::: ::::: :::::::::: :::::::: ::::: ::::::::: d1twda_ 109 MAAA--GPLAVTFHrAFDMCanPLYTLNNLAElGIARVLTS-gqkSDALQ-GLSKIMELI 164 d1tqja_ 159 QMCdergLDPWIEVDGGLKPNNTWQVLEAGANAIVAGsaVFNA-------------pnYA 205 ::: :::::::::::::::::::::::::::::: :::: :: d1twda_ 165 AHR----DAPIIMAGAGVRAENLHHFLDAGVLEVHSS--AGAWqaspmryrnysryivDG 218 d1tqja_ 206 EAIAGVR-NSKR---- 216 ::::::: :::: d1twda_ 219 AAVAEMKgIIERhqak 234 FAST alignment (Normalized score: 11.07 Raw score:2488.00) d1tqja_ 1 KNIVVAPSILSADFSR--LGEEIKAVDEAGADWIHVDVMDGRFVPNIT---------IGP 49 :::::: ::::::::::::::::::: ::: d1twda_ 1 --ALLEIC--------CYSMECALTAQQNGADRVELC-----------AAPKEGGLTPSL 39 d1tqja_ 50 LIVDAIRPLTKKTLDVHLMIV---------------EPEKYVEDFAKAGADIISVHVEHN 94 :::::::::::::::::: :::::::::::::::::::::: d1twda_ 40 GVLKSVRQRVTIPVHPII---RPRGGDFCYSDGEFAAILEDVRTVRELGFPGLVTGVL-- 94 d1tqja_ 95 ASP---------HLHRTLCQIRE-LGKKAGAVL---NPST--PLDFLEYVLP-VCDLILI 138 :::::::: ::::::: :::: :::::::::: :::::: d1twda_ 95 ---DVDGNVDMPRMEKIMAA---AGPLAVTF--HRAFDMCANPLYTLNNLAELGIARVL- 145 d1tqja_ 139 MSVNPQSF-------IPEVLPKIRALRQMCDERGLDPWIEVDGGLKPNNTWQVLEAGANA 191 ::::::::::::: :::::::::::::::::::::::::::: d1twda_ 146 --------TSGQKSDALQGLSKIMELIA----HRDAPIIMAGAGVRAENLHHFLDAGVLE 193 d1tqja_ 192 IVAGSAVFNAPN--------------------YAEAIAGVRNSKR--------- 216 ::: ::::::::: d1twda_ 194 VHS---------SAGAWQASPMRYRNYSRYIVDGAAVAEMK----GIIERHQAK 234 TMalign alignment (TM-score: 0.71 Raw score:154.18) d1tqja_ 1 KNIVVAPSILSADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITIGPL-IVDAIRPLT 59 :::::::: : :: :::::::::::::::::::: :::::::: ::::::::: d1twda_ 1 --ALLEICCY---S--ME-CALTAQQNGADRVELCAAPK---EGGLTPSLGVLKSVRQRV 49 d1tqja_ 60 KKTLDVHLMI------V----E--PEKYVEDFAKAGADIISVHVEHN--ASP-H-LHRTL 103 :::::::::: : : ::::::::::::::::::::::: ::: : ::::: d1twda_ 50 TIPVHPIIRPRGGDFCYSDGEFAAILEDVRTVRELGFPGLVTGVLDVDGNVDMPRMEKIM 109 d1tqja_ 104 CQIRELGKKAGAVLN-PST-PL-DFLEYVLP-VCDLILIMSVNPQSFIPEVLPKIRALRQ 159 ::: : ::::::::: ::: :: :::::::: ::::::::::: ::::::::::::::: d1twda_ 110 AAA-G-PLAVTFHRAFDMCANPLYTLNNLAELGIARVLTSGQK--SDALQGLSKIMELIA 165 d1tqja_ 160 MCDERGLDPWIEVDGGLKPNNTWQVLEAGANAIVAGSAV---------------FNAPNY 204 :: : : ::::::::::::::::::::::::::::::: :::::: d1twda_ 166 HR--D-A-PIIMAGAGVRAENLHHFLDAGVLEVHSSAGAWQASPMRYRNYSRYIVDGAAV 221 d1tqja_ 205 AEAIAGVRNSK--R 216 ::::::::::: d1twda_ 222 AEMKGIIERHQAK- 234 HHsearch alignment (Probability: 1.00 E-value:0.00) d1tqja_ 19 EEIKAVDEAGADWIHVDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHLM---------- 68 :::::::::::::: :::::::::::::::::::::::::::::::::: d1twda_ 11 ECALTAQQNGADRV--ELCAAPKEGGLTPSLGVLKSVRQRVTIPVHPIIRPRGGDFCYSD 68 d1tqja_ 69 --IVEPEKYVEDFAKAGADIISVHVEHNAS-PHLHRTLCQIRELGKKAGAVLNPSTPLDF 125 :::::::::::::::::::::::::::: :::::::::::: :::::::::::::: d1twda_ 69 GEFAAILEDVRTVRELGFPGLVTGVLDVDGNVDMPRMEKIMAA---AGPLAVTFHRAFDM 125 d1tqja_ 126 LEYVLPVCDLILIMSV---NPQSFIPEVLPKIRALRQMCDERGLDPWIEVDGGLKPNNTW 182 :::::::::::::::: ::::::::::::::::::::::: ::::::::::::::::: d1twda_ 126 CANPLYTLNNLAELGIARVLTSGQKSDALQGLSKIMELIAHR-DAPIIMAGAGVRAENLH 184 d1tqja_ 183 QVLEAGANAIVAGSAVFNAPNY-----------AEAIAGVRNS 214 :::::::::::::::::::::: :::::::::: d1twda_ 185 HFLDAGVLEVHSSAGAWQASPMRYRNYSRYIVDGAAVAEMKGI 227