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 <-- 1.718 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1rhca_) 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 d1rhca_ Coenzyme F420 dependent secondary alcohol dehydrogenaseBacterial luciferase-​likeTIM 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 <-- 1.718 --> Hit
DALI alignment (Z-score: 13.5 Raw score:1387.60) d1tqja_ 1 KNIVVAPSIL--sADFSRLGEEIKAVDEAGADWIHVDVMDG---rfvpnITIGPLIVDAI 55 :::::::::: :::::::::::::::::::::::::::: ::::::::::: d1rhca_ 1 MKTQIGYFASleqYRPMDALEQAIRAEKVGFDSVWVDDHFHpwyhdnaqSAQAWAWMGAA 60 d1tqja_ 56 RPLT-KKTLDV-HLMI--VEPE-KYVEDFAKAG-----aDIISVHVE------------- 92 :::: :::::: :::: :::: :::::::::: :::::::: d1rhca_ 61 LQATkKVFISTcITCPimRYNPaIVAQTFATLRqmypgrVGVAVGAGeamnevpvtgewp 120 d1tqja_ 93 --HNASPHLHRTLCQIREL---------------------------GKKAGAVLNpstPL 123 ::::::::::::::::: ::::::::: :: d1rhca_ 121 svPVRQDMTVEAVKVMRMLwesdkpvtfkgdyftldkaflytkpddEVPLYFSGM---GP 177 d1tqja_ 124 DFLEyvLPVCDLILIMSVnpqsFIPEVLP-KIRALRQMCDE-RGLD--PWIEVDGG---- 175 :::: :::::::::::: ::::::: ::::::::::: :::: :::::::: d1rhca_ 178 KGAKlaGMYGDHLMTVAA----APSTLKNvTIPKFEEGAREaGKDPskMEHAMLIWysvd 233 d1tqja_ 176 -------------------------------------------------------lKPNN 180 :::: d1rhca_ 234 pdydkavealrfwagclvpsmfkykvydpkevqlhanlvhcdtikenymcatdaeeMIKE 293 d1tqja_ 181 TWQVLEAGANAIVAGS----avfNAPNYAEAIAGVRNskr 216 :::::::::::::::: :::::::::::::: d1rhca_ 294 IERFKEAGINHFCLGNsspdvnfGIDIFKEVIPAVRD--- 330 FAST alignment (Normalized score: 9.37 Raw score:2500.00) d1tqja_ 1 KNIVVAPS--ILSADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITI----------- 47 :::::::: ::::::::::::::::::::::::::::: d1rhca_ 1 MKTQIGYFASLEQYRPMDALEQAIRAEKVGFDSVWVDDH----------FHPWYHDNAQS 50 d1tqja_ 48 --GPLIVDAIRPLT-KKTLDVHLMIVEPEK---------YVEDFAKAGA----------- 84 :::::::::::: :::::: ::::::: d1rhca_ 51 AQAWAWMGAALQATKKVFIST---------CITCPIMRYNPAIVAQ---TFATLRQMYPG 98 d1tqja_ 85 -DIISVHV----------------EHNASPHLHRTLCQIREL------------------ 109 :::::: ::::::::::::::::: d1rhca_ 99 RVGVAVG-AGEAMNEVPVTGEWPSVPVRQDMTVEAVKVMRM-LWESDKPVTFKGDYFTLD 156 d1tqja_ 110 ----------GKKAGAVLNPS-TPLDFLEYVLPVCDLILIMSVNPQSF----IPEVL-PK 153 ::::::: :::::::::::::::::: ::::: :: d1rhca_ 157 KAFLYTKPDDEVPLYFS----GMGPKGAKLAGMYGDHLMT--------VAAAPSTLKNVT 204 d1tqja_ 154 IRALRQMCDERGL---DPWIEVDGGL---------------------------------- 176 ::::::::::::: ::::::: d1rhca_ 205 IPKFEEGAREAGKDPSKMEHAML---IWYSVDPDYDKAVEALRFWAGCLVPSMFKYKVYD 261 d1tqja_ 177 ----------------------------KPNNTWQVLEAGANAIVAGSAVFNAPNYAE-- 206 :::::::::::::::::: ::::::::: d1rhca_ 262 PKEVQLHANLVHCDTIKENYMCATDAEEMIKEIERFKEAGINHFCL---GNSSPDVNFGI 318 d1tqja_ 207 -AIAGVRNSKR----- 216 :::::: d1rhca_ 319 DIFKEVI----PAVRD 330 TMalign alignment (TM-score: 0.74 Raw score:160.89) d1tqja_ 1 KNIVVAPSIL--SADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPN-----ITIGPLIVD 53 :::::::::: ::::::::::::::::::::::::::::: ::: ::::::::: d1rhca_ 1 MKTQIGYFASLEQYRPMDALEQAIRAEKVGFDSVWVDDHFH--PWYHDNAQSAQAWAWMG 58 d1tqja_ 54 AIRPLT-KKTLDVHLMIVE--P-E-KYVEDFAKAG-----ADIISVHV------------ 91 :::::: :::::::::::: : : :::::::::: :::::::: d1rhca_ 59 AALQATKKVFISTCITCPIMRYNPAIVAQTFATLRQMYPGRVGVAVGAGEAMNEVPVTGE 118 d1tqja_ 92 ---E-HN--ASPHLHRTLCQIRE---------------------L---GKKAGAVLNPST 121 : :: :::::::::::::: : :::::::: ::: d1rhca_ 119 WPSVPVRQDMTVEAVKVMRMLWESDKPVTFKGDYFTLDKAFLYTKPDDEVPLYFSG-MGP 177 d1tqja_ 122 P-LDFLEYVLPVCDLILIMSVNPQSFIPEVLPKIRALRQM-CDE--RGL-DPWIEVDGG- 175 : ::::::: ::::::::: ::::::::::::::: ::: ::: ::::::::: d1rhca_ 178 KGAKLAGMY---GDHLMTVAA----APSTLKNVTIPKFEEGAREAGKDPSKMEHAMLIWY 230 d1tqja_ 176 --------------------------------------------------LK-------P 178 :: : d1rhca_ 231 SVDPDYDKAVEALRFWAGCLVPSMFKYKVYDPKEVQLHANLVHCDTIKENYMCATDAEEM 290 d1tqja_ 179 -NNTWQVLEAGANAIVAGSAV-FNAPNYAEAIAGVRNSK-R 216 :::::::::::::::::::: ::::::::::::::::: d1rhca_ 291 IKEIERFKEAGINHFCLGNSSPDVNFGIDIFKEVIPAVRD- 330 HHsearch alignment (Probability: 0.14 E-value:0.02) d1tqja_ 179 NNTWQVLEAGANAIVAGSAVFNAPNYAEAIAGVRN 213 ::::::::::::::::::: ::::::::::::: d1rhca_ 292 KEIERFKEAGINHFCLGNS---SPDVNFGIDIFKE 323