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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1tqja_ | D-ribulose-5-phosphate 3-epimerase | Ribulose-phoshate binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1pe1a_ | 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase) | Aldolase | TIM beta/alpha-barrel | α/β |
Query <-- 2.347 --> IntermediateDALI 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 <-- 1.807 --> HitDALI alignment (Z-score: 14.4 Raw score:1375.70) d1tqja_ 1 -KNIVVAPSIL-sadFSRLGEEIKAVDEAG------aDWIHVDVMDgRFVP-----NITI 47 :::::::::: ::::::::::::::: ::::::::: :::: :::: d1pe1a_ 1 mEKFLVIAGPCaiesEELLLKVGEEIKRLSekfkeveFVFKSSFDK-ANRSsihsfRGHG 59 d1tqja_ 48 G---PLIVDAIRPLTKKTLDVHLmivEPEKYVEDFAKaGADIISVHVEhnaspHLHRTLC 104 : ::::::::::::::::::: ::::::::::: :::::::::: ::::::: d1pe1a_ 60 LeygVKALRKVKEEFGLKITTDI---HESWQAEPVAE-VADIIQIPAF---lcRQTDLLL 112 d1tqja_ 105 QIRELGKKAGAVLNPSTPLDFLEYVLPVC-------DLILIMS-vnpqsfIPEVLPKIRA 156 ::::::::::::::::::::::::::::: ::::::: :::::::::: d1pe1a_ 113 AAAKTGRAVNVKKGQFLAPWDTKNVVEKLkfggakeIYLTERGttfgynnLVVDFRSLPI 172 d1tqja_ 157 LRQMcdergldPWIEVDGG------------lKPNNTWQVLEAGANAIVAGS-------- 196 :::: :::::::: :::::::::::::::::::: d1pe1a_ 173 MKQW-------AKVIYDAThsvqlpgggmrefIFPLIRAAVAVGCDGVFMEThpepekal 225 d1tqja_ 197 ------AVFNApnYAEAIAGvRNSK----------r 216 ::::: ::::::: :::: d1pe1a_ 226 sdastqLPLSQ--LEGIIEA-ILEIrevaskyyeti 258 FAST alignment (Normalized score: 9.68 Raw score:2285.00) d1tqja_ 1 -KNIVVAPSILS----ADFSRLGEEIKAVDEAGA---------DWIHVDVMDGRFV---- 42 :::::::: ::::::::::::::: :::::: d1pe1a_ 1 MEKFLVIAG---PCAIESEELLLKVGEEIKR---LSEKFKEVEFVFKSS-------FDKA 47 d1tqja_ 43 ------PNITI----GPLIVDAIRPLTKKTLDVHLMIVE-PEKYVEDFAKAGADIISVHV 91 ::::: :::::::::::::::::::: :::::::::: :::::::: d1pe1a_ 48 NRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDI----HESWQAEPVAE-VADIIQIP- 101 d1tqja_ 92 EHNASPH-LHRTLCQIRELGKKAGAVLNPSTPLDFLEYVLPVC---------DLILIMSV 141 :::: ::::::::::::::::::::::::::::::::: :::::: d1pe1a_ 102 -AFLC--RQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVE--KLKFGGAKEIYLTER-- 154 d1tqja_ 142 NPQSFIPE-----------VLPKIRALRQMCDERGLDPWIEVDGGL-------------- 176 :::::::::: :::::: d1pe1a_ 155 --------GTTFGYNNLVVDFRSLPIMKQ-------WAKVIY----DATHSVQLPGGGMR 195 d1tqja_ 177 --KPNNTWQVLEAGANAIVAGSAVFN------------------APNYAEAIAGVRNSKR 216 :::::::::::::::::: :::::::::::: d1pe1a_ 196 EFIFPLIRAAVAVGCDGVFM------ETHPEPEKALSDASTQLPLSQLEGIIEAIL---- 245 d1tqja_ 217 ------------- 217 d1pe1a_ 246 EIREVASKYYETI 258 TMalign alignment (TM-score: 0.72 Raw score:155.62) d1tqja_ 1 -KNIVVAPSILSADF-SRLGEEIKAVDEAG------ADWIHVD-VMDGRFVP---NITI- 47 :::::::::::::: :::::::::::::: ::::::: :::: :: :::: d1pe1a_ 1 MEKFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKAN--RSSIHSFRGH 58 d1tqja_ 48 GP-LIVDAIR---PLTKKTLDVHLMIVEPEKYVEDFAKAGADIISVHVEHNASPHLHRTL 103 :: ::::::: ::::::::::: : :::::::::: :::::::::: ::::: ::: d1pe1a_ 59 GLEYGVKALRKVKEEFGLKITTDI-H--ESWQAEPVAE-VADIIQIPAF--LCRQT-DLL 111 d1tqja_ 104 CQIRELGKKAGAVLNPSTPLDFLEYVLP--V---C--DLILIMSVN---PQSFIPEVLPK 153 :::::::::::::::::::::::::::: : : ::::::::: ::::::::: d1pe1a_ 112 LAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGY--NNLVVDFRS 169 d1tqja_ 154 IRALRQMCDERGLDPWIEVD--G-G---------LKPNNTWQVLEAGANAIVAGS----- 196 ::::: :: :::::: : : ::::::::::::::::::::: d1pe1a_ 170 LPIMK-QW------AKVIYDATHSVQLPGGGMREFIFPLIRAAVAVGCDGVFMETHPEPE 222 d1tqja_ 197 -------AVFNAPNYAEAIAGVRNSK--R------- 216 ::::::::::::::::::: : d1pe1a_ 223 KALSDASTQLPLSQLEGIIEAILEIREVASKYYETI 258 HHsearch alignment (Probability: 0.75 E-value:0.00) d1tqja_ 1 KNIVVAPSILSADFSR-LGEEIKAVDEAGADWIHVD--VMDGRFVPNIT-------IG-- 48 :::::::::::::::: ::::::::::::::::::: ::::::::::: :: d1pe1a_ 2 EKFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLE 61 d1tqja_ 49 --PLIVDAIRPLTKKTLDVHLMIVEPEKYVEDFAKAGADIISVHVEHNASPHLHRTLCQI 106 :::::::::::::: :::::::::::::::::::::::::: ::: :::::::: d1pe1a_ 62 YGVKALRKVKEEFGLK----ITTDIHESWQAEPVAEVADIIQIPAF--LCR-QTDLLLAA 114 d1tqja_ 107 RELGKKAGAVLNPSTPLDFLEYVLPV------CDLILI--MSVNPQSFIPEVLPKIRALR 158 :::::::::::::::::::::::::: :::::: :::::::::::::::::::: d1pe1a_ 115 AKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMK 174 d1tqja_ 159 QMCDERGLDPWIEV---DGGLK---PNNTWQVLEAGANAIVAGSA 197 :::::::: ::::: ::::: :::::::::::::::::::: d1pe1a_ 175 QWAKVIYD-ATHSVQLPGGGMREFIFPLIRAAVAVGCDGVFMETH 218