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 <-- 2.035 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1geqa_) 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 d1geqa_ Trp synthase alpha-​subunitRibulose-​phoshate binding barrelTIM 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 <-- 2.035 --> Hit
DALI alignment (Z-score: 17.6 Raw score:1571.70) d1tqja_ 1 --KNIVVAPSIL--saDFSRLGEEIKAVDEaGADWIHVDVMDGRFV------PNIT---- 46 :::::::::: :::::::::::::: ::::::::::::::: :::: d1geqa_ 1 mfKDGSLIPYLTagdpDKQSTLNFLLALDE-YAGAIELGIPFSDPIadgktiQESHyral 59 d1tqja_ 47 -------iGPLIVDAIRPLTKKTLDVHLmIVEPEK------YVEDFAKAGADIISVHveh 93 :::::::::::::::::::: :::::: :::::::::::::::: d1geqa_ 60 kngfklreAFWIVKEFRRHSSTPIVLMT-YYNPIYragvrnFLAEAKASGVDGILVV--- 115 d1tqja_ 94 nASPH--LHRTLCQIRELGKKAGAVLNPSTPLDFLEYVLPVCD-LILIMSVNpqSFIPEV 150 :::: :::::::::::::::::::::::::::::::::::: :::::::: :::::: d1geqa_ 116 -DLPVfhAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTgFVYLVSLY--EIPKTA 172 d1tqja_ 151 LPKIRALRQMCderglDPWIEVDGGLKPN-NTWQVLEAGANAIVAGSAVFNA-------- 201 ::::::::::: ::::::::::::: :::::::::::::::::::::: d1geqa_ 173 YDLLRRAKRIC-----RNKVAVGFGVSKReHVVSLLKEGANGVVVGSALVKIigekgrea 227 d1tqja_ 202 -PNYAEAIAGVRNskr 216 :::::::::::: d1geqa_ 228 tEFLKKKVEELLG--i 241 FAST alignment (Normalized score: 14.01 Raw score:3196.00) d1tqja_ 1 K---NIVVAPSILSA------DFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITI---- 47 ::::::: :::::::::::::: :::::::::::: d1geqa_ 1 -MFKDGSLIPY----LTAGDPDKQSTLNFLLALDE-YAGAIELGIPFS--------DPIA 46 d1tqja_ 48 ---------------------GPLIVDAIRPLTKKTLDVHLMI------VEPEKYVEDFA 80 ::::::::::::::::::::: ::::::::::: d1geqa_ 47 DGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTY-YNPIYRAGVRNFLAEAK 105 d1tqja_ 81 KAGADIISVHVEHN---ASPHLHRTLCQIRELGKKAGAVLNPSTPLDFLEYVLPVC-DLI 136 ::::::::: ::::::::::::::::::::::::::::::::::::::: ::: d1geqa_ 106 ASGVDGILV-----VDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFV 160 d1tqja_ 137 LIMSVN-PQSFIPEVLPKIRALRQMCDERGL-DPWIEVDGGL-KPNNTWQVLEAGANAIV 193 ::: :::::::::::::::::: :::::::::: ::::::::::::::::: d1geqa_ 161 YLV---SLYEIPKTAYDLLRRAKRI------CRNKVAVGFGVSKREHVVSLLKEGANGVV 211 d1tqja_ 194 AGSAVFNAP------------NYAEAIAGVRNSKR--- 216 :::::: ::::::::: d1geqa_ 212 VGSALV---KIIGEKGREATEFLKKKVEEL-----LGI 241 TMalign alignment (TM-score: 0.75 Raw score:161.77) d1tqja_ 1 --KNIVVAPSILS-ADF-SRLGEEIKAVDEAGADWIHVDVMDGRFVP-----N--I--T- 46 ::::::::::: ::: :::::::::::: :::::::::::::::: : : : d1geqa_ 1 MFKDGSLIPYLTAGDPDKQSTLNFLLALDE-YAGAIELGIPFSDPIADGKTIQESHYRAL 59 d1tqja_ 47 ---I-GPLIVDAIRPL---TKKTLDVHLMIVEPE---K--YVEDFAKAGADIISVHVEHN 94 : ::::::::::: ::::::::::::::: : :::::::::::::::: : : d1geqa_ 60 KNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIYRAGVRNFLAEAKASGVDGILVV-D-L 117 d1tqja_ 95 ASPHLHRTLCQIRELGKKAGAVLNPSTPLDFLEYVLPVC-DLILIMSVNPQSFIPEVLPK 153 ::::::::::::::::::::::::::::::::::::::: ::::::::: ::::::::: d1geqa_ 118 PVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLY--EIPKTAYDL 175 d1tqja_ 154 IRALRQMCDERGLDPWIEVDGGLK-PNNTWQVLEAGANAIVAGSAVF-N---------AP 202 :::::::: : :::::::::: :::::::::::::::::::::: : :: d1geqa_ 176 LRRAKRIC----R-NKVAVGFGVSKREHVVSLLKEGANGVVVGSALVKIIGEKGREATEF 230 d1tqja_ 203 NYAEAIAGVRNSKR 216 :: ::::::::: d1geqa_ 231 LK-KKVEELLGI-- 241 HHsearch alignment (Probability: 0.99 E-value:0.00) d1tqja_ 4 VVAPSILSA--DFSRLGEEIKAVDEAGADWIHVDV------MDGRFVPNIT--------- 46 ::::::::: :::::::::::: ::::::::::: :::::::::: d1geqa_ 6 SLIPYLTAGDPDKQSTLNFLLAL-DEYAGAIELGIPFSDPIADGKTIQESHYRALKNGFK 64 d1tqja_ 47 --IGPLIVDAIRPLTKKTLDVHLMIVEP------EKYVEDFAKAGADIISVHVEHNASPH 98 ::::::::::::::::::: :::::: ::::::::::::::::::: ::::: d1geqa_ 65 LREAFWIVKEFRRHSSTPIVL-MTYYNPIYRAGVRNFLAEAKASGVDGILVVD--LPVFH 121 d1tqja_ 99 LHRTLCQIRELGKKAGAVLNPSTPLDFLEYVLPVCD----LILIMSVNPQSFIPEVLPKI 154 :::::::::::::::::::::::::::::::::::: :::::::::: : :::: d1geqa_ 122 AKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYEIPKT--A---YDLL 176 d1tqja_ 155 RALRQMCDERGLDPWIEVDGGLK-PNNTWQVLEAGANAIVAGSAVFN 200 :::::: :::::::::::: ::::::::::::::::::::::: d1geqa_ 177 RRAKRI-----CRNKVAVGFGVSKREHVVSLLKEGANGVVVGSALVK 218