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 <-- 1.916 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1eyea_) 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 d1eyea_ Dihydropteroate synthetaseDihydropteroate synthetase-​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 <-- 1.916 --> Hit
DALI alignment (Z-score: 13.1 Raw score:1251.90) d1tqja_ 1 kNIVVAPSIL--------SADF---SRLGEEIKAVDEAGADWIHVDVMdgrfvpniTIGP 49 ::::::::: :::: ::::::::::::::::::::::: :::: d1eyea_ 1 -PVQVMGVLNvtddsfsdGGCYldlDDAVKHGLAMAAAGAGIVDVGGE-------tSRVI 52 d1tqja_ 50 LIVDAIRPLtKKTLDVHLMivePEKYVEDFAKAGADIISVHVehnASPHlhRTLCQIREL 109 ::::::::: ::::::::: :::::::::::::::::::: :::: ::::::::: d1eyea_ 53 PVVKELAAQ-GITVSIDTM---RADVARAALQNGAQMVNDVS-ggRADP--AMGPLLAEA 105 d1tqja_ 110 GKKAGAVLN-----------------pstPLDFLEYVL---------PVCDLILIMSVN- 142 ::::::::: ::::::::: :::::::::::: d1eyea_ 106 DVPWVLMHWravsadtphvpvrygnvvaeVRADLLASVadavaagvdPARLVLDPGLGFa 165 d1tqja_ 143 -pqsfIPEVLPKIRALRQMCdergldPWIEVDGGL------------------------K 177 ::::::::::::::: ::::::::: : d1eyea_ 166 ktaqhNWAILHALPELVATG------IPVLVGASRkrflgallagpdgvmrptdgrdtaT 219 d1tqja_ 178 PNNTWQVLEAGANAIVAGSavfnapnyaEAIAGVRNSK------r 216 ::::::::::::::::::: :::::::::: d1eyea_ 220 AVISALAALHGAWGVRVHD--------vRASVDAIKVVeawmgae 256 FAST alignment (Normalized score: 9.54 Raw score:2244.00) d1tqja_ 1 KNIVVAPSILSADF-----------------SRLGEEIKAVDEAGADWIHVDVMDGRFVP 43 ::::::: ::::::::::::::::::::: d1eyea_ 1 -PVQVMGV------LNVTDDSFSDGGCYLDLDDAVKHGLAMAAAGAGIVDVG-------- 45 d1tqja_ 44 NITI-----GPLIVDAIRPLTKKTLDVHLMIVE-PEKYVEDFAKAGADIISVHVEHN--- 94 :::::::::: ::::::::: :::::::::::::::::: d1eyea_ 46 ----GETSRVIPVVKELAA-QGITVSIDT----MRADVARAALQNGAQMVND-----VSG 91 d1tqja_ 95 --ASPHLHRTLCQIRELGKKAGAVLNPST----------------------PLDFLEYVL 130 ::::::::::: :::::::: ::::::::: d1eyea_ 92 GRADPAMGPLLAE---ADVPWVLM-----HWRAVSADTPHVPVRYGNVVAEVRADLLASV 143 d1tqja_ 131 PVC-----------DLILIMSVNPQSF--------IPEVLPKIRALRQMCDERGLDPWIE 171 : ::::::: ::::::::::::: :::::: d1eyea_ 144 A--DAVAAGVDPARLVLDPGL------GFAKTAQHNWAILHALPELVA------TGIPVL 189 d1tqja_ 172 VDGGL---------------------------KPNNTWQVLEAGANAIVAGSAVFNAPNY 204 :: ::::::::::::::::::: d1eyea_ 190 VG---ASRKRFLGALLAGPDGVMRPTDGRDTATAVISALAALHGAWGVRVH--------- 237 d1tqja_ 205 AEAIAGVRNSKR------------- 216 :::::: d1eyea_ 238 --DVRASV----DAIKVVEAWMGAE 256 TMalign alignment (TM-score: 0.69 Raw score:148.32) d1tqja_ 1 KNIVVAPSIL--------SADF-S--RLGEEIKAVDEAGADWIHVDVMDGRFVPNITIGP 49 ::::::::: :::: : :::::::::::::::::::: ::: d1eyea_ 1 -PVQVMGVLNVTDDSFSDGGCYLDLDDAVKHGLAMAAAGAGIVDVG-----------GET 48 d1tqja_ 50 L-IVDAIRPL--TKKTLDVHLMIVEPEKYVEDFAKAGADIISV-HVEHNASPHLHRTLCQ 105 : :::::::: ::::::::: : :::::::::::::::::: :::: :: : ::::: d1eyea_ 49 SRVIPVVKELAAQGITVSIDT-M--RADVARAALQNGAQMVNDVSGGR-AD-P--AMGPL 101 d1tqja_ 106 IRELGKKAGAVLNP---------------S--TPLDFLEY-VL-------PV-CDLILIM 139 :::::::::::::: : :::::::: :: :: ::::::: d1eyea_ 102 LAEADVPWVLMHWRAVSADTPHVPVRYGNVVAEVRADLLASVADAVAAGVDPARLVLDPG 161 d1tqja_ 140 SVNP-QSF-IPEVLPKIRALRQMCDERGLDPWIEVDGG---------------------- 175 :::: ::: ::::::::::::::: :::::::: d1eyea_ 162 LGFAKTAQHNWAILHALPELVATG------IPVLVGASRKRFLGALLAGPDGVMRPTDGR 215 d1tqja_ 176 --LKPNNTWQVLEAGANAIVAGSAVFNAPNYAEAIAGVRNSK--R---- 216 :::::::::::::::::::: : : :::::::::: : d1eyea_ 216 DTATAVISALAALHGAWGVRVH--D-----V-RASVDAIKVVEAWMGAE 256 HHsearch alignment (Probability: 0.74 E-value:0.01) d1tqja_ 12 ADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHLMIVE 71 ::::::::::::::::::::: :::: ::::::::::::::: ::::::: ::: d1eyea_ 22 LDLDDAVKHGLAMAAAGAGIV--DVGG-----ETSRVIPVVKELAAQ-GITVSID--TMR 71 d1tqja_ 72 PEKYVEDFAKAGADIIS-VHVEHNASPHLHRTLCQIRELGKKAGAVLNPSTP 122 :::::::::::::::: :::: : ::::::::::::::::::::::::: d1eyea_ 72 -ADVARAALQNGAQMVNDVSGG--R--ADPAMGPLLAEADVPWVLMHWRAVS 118