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 <-- 1.950 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1juba_) 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 d1juba_ Dihydroorotate dehydrogenaseFMN-​linked oxidoreductasesTIM 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 <-- 1.950 --> Hit
DALI alignment (Z-score: 13.7 Raw score:1380.00) d1tqja_ 1 ----------kNIVVAPSILSAdfsrLGEEIKAVDEAGADWIHVDVMD------------ 38 ::::::::::: :::::::::::::::::::::: d1juba_ 1 mlnttfanakfANPFMNASGVH--cmTIEDLEELKASQAGAYITKSSTlekregnplpry 58 d1tqja_ 39 -------grfvPNIT-IGPLIVDAIRPL-----TKKTLDVHLMIVE---PEKYVEDFAKA 82 :::: :::::::::::: ::::::::::::: ::::::::::: d1juba_ 59 vdlelgsinsmGLPNlGFDYYLDYVLKNqkenaQEGPIFFSIAGMSaaeNIAMLKKIQES 118 d1tqja_ 83 -gaDIISVHVE-------HNAS---pHLHRTLCQIRE-LGKKAGAVLNPS---tPLDFL- 126 :::::::: :::: ::::::::::: :::::::::::: ::::: d1juba_ 119 dfsGITELNLScpnvpgePQLAydfeATEKLLKEVFTfFTKPLGVKLPPYfdlvHFDIMa 178 d1tqja_ 127 EYVLPV-CDLILIMSV-----------------------NPQS--FIPEVLPKIRALRQM 160 :::::: ::::::::: :::: ::::::::::::::: d1juba_ 179 EILNQFpLTYVNSVNSignglfidpeaesvvikpkdgfgGIGGayIKPTALANVRAFYTR 238 d1tqja_ 161 CDergLDPWIEVDGGLKPN-NTWQVLEAGANAIVAGSAVFNApnYAEAIAGVRNSK---- 215 :: :::::::::::::: :::::::::::::::::::::: :::::::::::: d1juba_ 239 LK---PEIQIIGTGGIETGqDAFEHLLCGATMLQIGTALHKE--GPAIFDRIIKELeeim 293 d1tqja_ 216 -----------------r 216 d1juba_ 294 nqkgyqsiadfhgklksl 311 FAST alignment (Normalized score: 9.62 Raw score:2493.00) d1tqja_ 1 KNI-------------VVAPSILSADFSR----LGEEIKAVDEAGADWIH-VDVMDGRFV 42 ::::::: ::::::::::::::::: :::: d1juba_ 1 ---MLNTTFANAKFANPFMNASG------VHCMTIEDLEELKASQAGAYITKSST----- 46 d1tqja_ 43 -----------------------PNITI----GPLIVDAIRP--LTKKTLDVHLMIV--- 70 ::::: :::::::::: ::::::::::::: d1juba_ 47 LEKREGNPLPRYVDLELGSINSMGLPNLGFDYYLDYVLKNQKENAQEGPIFFSIAGMSAA 106 d1tqja_ 71 EPEKYVEDFAKAGA-DIISVHVEHNAS---------------PHLHRTLCQIR-ELGKKA 113 :::::::::::::: ::::::: ::::::::::: :::::: d1juba_ 107 ENIAMLKKIQESDFSGITELNL-----SCPNVPGEPQLAYDFEATEKLLKEVFTFFTKPL 161 d1tqja_ 114 GAVLNPST----------PLDFLEYVLPVCDLILIMSVNPQSF----------------- 146 ::::: ::::::: ::::::: d1juba_ 162 GVKLP---PYFDLVHFDIMAEILNQ--FPLTYVN---------SVNSIGNGLFIDPEAES 207 d1tqja_ 147 -----------------IPEVLPKIRALRQMCDERGLDPWIEVDGGL-KPNNTWQVLEAG 188 :::::::::::::: ::: :::::::::: :::::::::::: d1juba_ 208 VVIKPKDGFGGIGGAYIKPTALANVRAFYTR--LKP-EIQIIGTGGIETGQDAFEHLLCG 264 d1tqja_ 189 ANAIVAGSAVFNAPNYAEAIAGVRNSKR------------------------- 216 ::::::::::: ::::::::::: d1juba_ 265 ATMLQIGTALH--KEGPAIFDRII----KELEEIMNQKGYQSIADFHGKLKSL 311 TMalign alignment (TM-score: 0.74 Raw score:160.28) d1tqja_ 1 ---KN-------IVVAPSILSAD-FSRLGEEIKAVDEAGADWIHVDVMD-----GR---- 40 :: ::::::::::: ::::::::::: : :::::::::: :: d1juba_ 1 MLNTTFANAKFANPFMNASGVHCMTIEDLEELKAS--Q-AGAYITKSSTLEKREGNPLPR 57 d1tqja_ 41 ----------FVPNITI-GP-LIVDAIRPL----TK-KTLDVHLMIV-E--PEKYVEDFA 80 :::::: :: ::::::::: :: :::::::::: : ::::::::: d1juba_ 58 YVDLELGSIN-SMGLPNLGFDYYLDYVLKNQKENAQEGPIFFSIAGMSAAENIAMLKKIQ 116 d1tqja_ 81 -KAGADIISV-H----------VE-HN-AS-PHLHRTLCQIRELGKKAGAVLNPST---P 122 ::::::::: : :: :: :: ::::::::::: ::::::::::: : d1juba_ 117 ESDFSGITELNLSCPNVPGEPQLAYDFEATEKLLKEVFTFFT---KPLGVKLPPYFDLVH 173 d1tqja_ 123 L-DFLEYVL-PVCDLILIMSVN----------------------P-QSF-I-PEVLPKIR 155 : ::::::: :::::::::::: : ::: : :::::::: d1juba_ 174 FDIMAEILNQFPLTYVNSVNSIGNGLFIDPEAESVVIKPKDGFGGIGGAYIKPTALANVR 233 d1tqja_ 156 ALRQMCDERGLDPWIEVDGGLKPN-NTWQVLEAGANAIVAGSAVF-NAPNYAEAIAGVRN 213 :::::: : :::::::::::::: :::::::::::::::::::: :::::::::::::: d1juba_ 234 AFYTRL--K-PEIQIIGTGGIETGQDAFEHLLCGATMLQIGTALHKEGPAIFDRIIKELE 290 d1tqja_ 214 SKR------------------ 216 ::: d1juba_ 291 EIMNQKGYQSIADFHGKLKSL 311 HHsearch alignment (Probability: 0.98 E-value:0.00) d1tqja_ 7 PSILSADFS-RLGEEIKAVDEAGADWI----------------HVDVMDGRFVPNITIGP 49 ::::::::: ::::::::::::::::: ::::::::::::::::: d1juba_ 14 PFMNASGVHCMTIEDLEELKASQAGAYITKSSTLEKREGNPLPRYVDLELGSINSMGLPN 73 d1tqja_ 50 LIVDA--------IRP-LTKKTLDVHLMIVEPEKYVEDFAK---AG-ADIISVHVEH--- 93 ::::: ::: :::::::::::::::::::::::: :: :::::::::: d1juba_ 74 LGFDYYLDYVLKNQKENAQEGPIFFSIAGMSAAENIAMLKKIQESDFSGITELNLSCPNV 133 d1tqja_ 94 -------NASPHLHRTLCQIRELG-KKAGAVLNPSTPLDFLEYVLPV-----CDLILIMS 140 ::::::::::::::::: :::::::::::::::::::::: :::::::: d1juba_ 134 PGEPQLAYDFEATEKLLKEVFTFFTKPLGVKLPPYFDLVHFDIMAEILNQFPLTYVNSVN 193 d1tqja_ 141 VN-------------------------PQSFIPEVLPKIRALRQMCDERGLDPWIEVDGG 175 :: :::::::::::::::::: :::::::::::: d1juba_ 194 SIGNGLFIDPEAESVVIKPKDGFGGIGGAYIKPTALANVRAFYTR---LKPEIQIIGTGG 250 d1tqja_ 176 L-KPNNTWQVLEAGANAIVAGSAVFNA-PNYAE 206 : ::::::::::::::::::::::::: ::::: d1juba_ 251 IETGQDAFEHLLCGATMLQIGTALHKEGPAIFD 283