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 <-- 2.078 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1hl2a_) 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 d1hl2a_ N-​acetylneuraminate lyaseAldolaseTIM 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 <-- 2.078 --> Hit
DALI alignment (Z-score: 15.1 Raw score:1474.60) d1tqja_ 1 -knIVVAPSIlsADFS---------RLGEEIKAVDEAGADWIHVDV----MDGRfvpnit 46 ::::::: :::: ::::::::::::::::::::: :::: d1hl2a_ 1 tnlRGVMAAL--LTPFdqqqaldkaSLRRLVQFNIQQGIDGLYVGGstgeAFVQ---sls 55 d1tqja_ 47 IGPLIVDAIRPLT--KKTLDVHLMIVE---PEKYVEDFAKAGADIISVHVEHN---asPH 98 ::::::::::::: :::::::::::: ::::::::::::::::::::::: :: d1hl2a_ 56 EREQVLEIVAEEAkgKIKLIAHVGCVStaeSQQLAASAKRYGFDAVSAVTPFYypfsfEE 115 d1tqja_ 99 LHRTLCQIRE--LGKKAGAVLNP-----STPLDFLEYVLPV--CDLILIMSvnpqsfipE 149 :::::::::: ::::::::::: ::::::::::::: :::::::: : d1hl2a_ 116 HCDHYRAIIDsaDGLPMVVYNIParsgvKLTLDQINTLVTLpgVGALKQTS--------G 167 d1tqja_ 150 VLPKIRALRQMCDerglDPWIEVDGGLkpnNTWQVLEAGANAIVAGsAVFNapnyaeAIA 209 ::::::::::::: :::::::::: :::::::::::::::: :::: ::: d1hl2a_ 168 DLYQMEQIRREHP----DLVLYNGYDE---IFASGLLAGADGGIGS-TYNI------MGW 213 d1tqja_ 210 GVR-NSKR---------------------------------------------------- 216 ::: :::: d1hl2a_ 214 RYQgIVKAlkegdiqtaqklqtecnkvidlliktgvfrglktvlhymdvvsvplcrkpfg 273 d1tqja_ 217 ---------------------- 217 d1hl2a_ 274 pvdekylpelkalaqqlmqerg 295 FAST alignment (Normalized score: 10.55 Raw score:2663.00) d1tqja_ 1 KN---IVVAPSILS----------ADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITI 47 :::::: :::::::::::::::::::::: d1hl2a_ 1 --TNLRGVMAA---LLTPFDQQQALDKASLRRLVQFNIQQGIDGLY-------------- 41 d1tqja_ 48 ---------------GPLIVDAIRPLT---KKTLDVHLMIV---EPEKYVEDFAKAGADI 86 ::::::::::: ::::::::::: :::::::::::::::: d1hl2a_ 42 VGGSTGEAFVQSLSEREQVLEIVAEE-AKGKIKLIAHVGCVSTAESQQLAASAKRYGFDA 100 d1tqja_ 87 ISVHVEHNAS---------PHLHRTLCQIRE--LGKKAGAVLN------PSTPLDFLEYV 129 :::: :::::::::::: ::::::::: ::::::::::: d1hl2a_ 101 VSAV------TPFYYPFSFEEHCDHYRAIIDSADGLPMVVYN-IPARSGVKLTLDQINTL 153 d1tqja_ 130 L--PVCDLILIMSVNPQSFIPE---VLPKIRALRQMCDERG-LDPWIEVDGGLKPNNTWQ 183 : :::::::: ::::::::::: :::::::: ::::::: d1hl2a_ 154 VTLPGVGALKQ-----------TSGDLYQMEQIRRE-----HPDLVLYNG---YDEIFAS 194 d1tqja_ 184 VLEAGANAIVAGSAVFNAPNYAE-AIAGVRNSKR-------------------------- 216 ::::::::::: :::: :::::: d1hl2a_ 195 GLLAGADGGIG-STYN-------IMGWRYQ----GIVKALKEGDIQTAQKLQTECNKVID 242 d1tqja_ 217 ----------------------------------------------------- 217 d1hl2a_ 243 LLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQERG 295 TMalign alignment (TM-score: 0.73 Raw score:158.65) d1tqja_ 1 -KNIVVAPSILSADF------S--RLGEEIKAVDEAGADWIHVDVM--DGRFVPNIT--- 46 :::::::::: ::: : :::::::::::::::::::::: ::::: d1hl2a_ 1 TNLRGVMAALL-TPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTG----EAFVQSLS 55 d1tqja_ 47 IGPLIVDAIRPLT-K-KTLDVHLMIV-E--PEKYVEDFAKAGADIISVHVE----HN--A 95 ::::::::::::: : :::::::::: : ::::::::::::::::::::: :: : d1hl2a_ 56 EREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEE 115 d1tqja_ 96 SPHLHRTLCQIRELGKKAGAVLNP-----STPLDFLEYV-LPV-CDLILIMSVNPQSFIP 148 :::::::::::: ::::::::::: :::::::::: ::: :::::::: : d1hl2a_ 116 HCDHYRAIIDSA-DGLPMVVYNIPARSGVKLTLDQINTLVTLPGVGALKQTS-------G 167 d1tqja_ 149 EVLPKIRALRQMCDERGLDPWIEVDGGLKPNNTWQVLEAGANAIVAGSAVFNAPNYAEAI 208 ::::::::::::: :::::::: :: ::::::::::::::::: :::: : ::: d1hl2a_ 168 -DLYQMEQIRREHP----DLVLYNGY-DE--IFASGLLAGADGGIGST-YNIM--G-WRY 215 d1tqja_ 209 AGVRNS--------KR-------------------------------------------- 216 :::::: :: d1hl2a_ 216 QGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPV 275 d1tqja_ 217 -------------------- 217 d1hl2a_ 276 DEKYLPELKALAQQLMQERG 295 HHsearch alignment (Probability: 0.85 E-value:0.00) d1tqja_ 11 SADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITIGPL----IVDAIRPLTK--KTLD 64 ::::::::::::::::::::::::::::: :::::::: :::::::::: :::: d1hl2a_ 19 ALDKASLRRLVQFNIQQGIDGLYVGGSTG---EAFVQSLSEREQVLEIVAEEAKGKIKLI 75 d1tqja_ 65 VHLM---IVEPEKYVEDFAKAGADIISVHVEHNASPHLHRTLCQIRE---LGKKAGAVL- 117 :::: :::::::::::::::::::::::::::::::::::::::: ::::::::: d1hl2a_ 76 AHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVY 135 d1tqja_ 118 -NPS-----TPLDFLEYVLPVCDLILIMSVNPQSFIPEVLPKIRALRQMCDERGLDPWIE 171 ::: :::::::::::::: :::: :::::::::::::::::: : :: d1hl2a_ 136 NIPARSGVKLTLDQINTLVTLPG---VGAL---KQTSGDLYQMEQIRREHP----D--LV 183 d1tqja_ 172 VDGGLKPNNTWQVLEAGANAIVAGSAVFNAPNYAEAIAGV 211 :::::: ::::::::::::::::::::::::::::::::: d1hl2a_ 184 LYNGYD-EIFASGLLAGADGGIGSTYNIMGWRYQGIVKAL 222