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 <-- 1.316 --> Intermediate <-- 1.020 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1v8aa_) through the intermediate protein (d1hl2a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1hl2a_ N-​acetylneuraminate lyaseAldolaseTIM beta/​alpha-​barrelα/β
Hit d1v8aa_ Hydroxyethylthiazole kinase (THZ kinase,​ ThiK)Ribokinase-​likeRibokinase-​likeα/β

Supporting Alignments

Query <-- 1.316 --> Intermediate
DALI alignment (Z-score: 8.3 Raw score:892.10) query 1 mietpyylidkakltrnmeriahvreksgaKALLALKCF----------aTWSVFDLMRD 50 ::::::::: :::::::::: d1hl2a_ 1 --------------------------tnlrGVMAALLTPfdqqqaldkasLRRLVQFNIQ 34 query 51 -YMDGTTSS-------------SLFEVRLGRERFG--KETHAYSVA----YGDNEIDEVV 90 :::::::: ::::::::::::: ::::::::: :::::::::: d1hl2a_ 35 qGIDGLYVGgstgeafvqslseREQVLEIVAEEAKgkIKLIAHVGCvstaESQQLAASAK 94 query 91 S-HADKIIFNS-----------ISQLERFADKAAGIARGLRLNPQRL-geWDVPKVERVM 137 : ::::::::: ::::::::::::::::::::::::: :::::::::: d1hl2a_ 95 RyGFDAVSAVTpfyypfsfeehCDHYRAIIDSADGLPMVVYNIPARSgvkLTLDQINTLV 154 query 138 DR--INGFMIHNncenkdfglfdrMLGEIEErFGALIARVdWVSLGGGIhftgddypvda 195 :: :::::::: ::::::: :::::::: :::::::: d1hl2a_ 155 TLpgVGALKQTS-----------gDLYQMEQ-IRREHPDL-VLYNGYDE----------- 190 query 196 fsARLRAFSdrygvqIYLEPGEASITksttlevtvldtlynknlaivdssieahmldlli 255 ::::::: ::::::::::: d1hl2a_ 191 ifASGLLAG-----aDGGIGSTYNIM---------------------------------- 211 query 256 yretakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwf 315 d1hl2a_ 212 ---------gwryqgivkalkegdiqtaqklqtecnkvidlliktgvfrglktvlhymdv 262 query 316 ngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1hl2a_ 263 vsvplcrkpfgpvdekylpelkalaqqlmqerg 295 FAST alignment (Normalized score: 3.89 Raw score:1246.00) query 1 MIETP----------------YYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSV 44 :::::::::::::::::: d1hl2a_ 1 -----TNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQ--------------------- 34 query 45 FDLMRD-YMDGTTSS---------------SLFEVRLGRERF--GKETHAYSVA--YGDN 84 :::::: :::::::::::: :::::::: :::: d1hl2a_ 35 ------QGIDGLY--VGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHV--GCVSTA 84 query 85 EIDEVVS-----HADKIIFN------------SISQLERFADKAAGIARGLRLNPQRLGE 127 ::::::: ::::::: ::::::::::::::::::::::: d1hl2a_ 85 ESQQLAASAKRYGFDAVSA-VTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIP----- 138 query 128 ------WDVPKVERV--MDRINGFMIHNNCENKDFGLFDRMLGE--IEERFGALIARV-- 175 ::::::::: :::::::::: :::::::::::: d1hl2a_ 139 ARSGVKLTLDQINTLVTLPGVGALKQT-----------------SGDLYQMEQIRREHPD 181 query 176 DWVSLGGGIHFTGDD-----------------------YPVDAFSARLRAFSDRYGVQIY 212 ::::: :::::::::::::: d1hl2a_ 182 LVLYN----------GYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALK-------- 223 query 213 LEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYM 272 d1hl2a_ 224 ------------------------------------------------------------ 224 query 273 ICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSV 332 d1hl2a_ 224 ------------------------------------------------------------ 224 query 333 RTVREFTYADYEQSLS-------------------------------------------- 348 d1hl2a_ 224 ----------------EGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPL 267 query 349 ---------------------------- 349 d1hl2a_ 268 CRKPFGPVDEKYLPELKALAQQLMQERG 295 TMalign alignment (TM-score: 0.43 Raw score:149.67) query 1 ---------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALK--CF--A- 40 :::::::::::::::::::: :: :::::::: :: : d1hl2a_ 1 TNLRGVMAALLTPFD----QQQALDKASLRRLVQFNIQQ--GI-DGLYVGGSTGEAFVQS 53 query 41 --T-WSVFDLMRDYM-----DGTTSSS--L-FEVRLGRER--FGKETHAYSVA------- 80 : ::::::::::: ::::::: : ::::::::: ::::::::::: d1hl2a_ 54 LSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSF 113 query 81 -YGDNEIDEVVS-H--ADKIIFN--------S-ISQLERFADKAAGIARGLRLNPQRLGE 127 ::::::::::: : ::::::: : ::::::::: :::::::::::: :: d1hl2a_ 114 EEHCDHYRAIIDSADGLPMVVYNIPARSGVKLTLDQINTLVT-LPGVGALKQTSG---DL 169 query 128 WDVPKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFT 187 ::::::::::: ::::::::: : :::::::::: :::::::::: d1hl2a_ 170 YQMEQIRREHP-DLVLYNGYD-----------E--IFASGLLAGA----DGGIGSTYNI- 210 query 188 GDDYPVDAFSARLRAFSDRYG------------------------VQIYLEPGE-AS--I 220 : ::::::::::::: ::: :: : d1hl2a_ 211 -----M--GWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTG------VFRGLKTVL 257 query 221 T----KSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKV-------------- 262 : ::::: ::::: ::::: d1hl2a_ 258 HYMDVVSVPL----------------------CRKPF----GPVDEKYLPELKALAQQLM 291 query 263 ----LPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGV 318 d1hl2a_ 292 QERG-------------------------------------------------------- 295 query 319 KMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1hl2a_ 296 ------------------------------ 296 HHsearch alignment (Probability: 0.05 E-value:0.04) query 1 MIETPYYL-IDKAKLTRNMERIAHVREKSGAKAL---LALKCFATWSVFDLMRD 50 :::::::: ::::::::::::::::::::::::: ::::::::::::::::: d1hl2a_ 102 SAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPARSGVKLTLDQINTLVT 155
Intermediate <-- 1.020 --> Hit
DALI alignment (Z-score: 3.5 Raw score:565.00) d1hl2a_ 1 -----------tnlrgvMAAL---------------------LTPFdqqqaldKASLRRL 28 :::: :::: ::::::: d1v8aa_ 1 mkfiiealkrvrerrplVHNItnfvvmnttanallalgaspvMAHA-------EEELEEM 53 d1hl2a_ 29 VQFNIqqgidGLYVGgstgeAFVQSlSEREQVLEIVAEEAKG-KIKLIAHVGC-vSTAES 86 ::::: ::::: ::::: :::::::::::::::: :::::::::: ::::: d1v8aa_ 54 IRLAD-----AVVIN-----IGTLD-SGWRRSMVKATEIANElGKPIVLDPVGagATKFR 102 d1hl2a_ 87 QQLAASAKRYGFDAVSAvtpfyypfsfeehCDHYRAIIDSadglpmvvyniparsgvklt 146 ::::::::::::::::: :::::::::: d1v8aa_ 103 TRVSLEILSRGVDVLKG------------nFGEISALLGE-------------------- 130 d1hl2a_ 147 ldQINTLVTL--PGVG----alkqtsgdlyqmeqirrEHPD------------------- 181 :::::::: :::: :::: d1v8aa_ 131 egGEEEAKKLtmNAARefnttvavtgavdyvsdgrrtFAVYnghellgrvtgtgcmvaal 190 d1hl2a_ 182 -------------lVLYN----------------------gYDEIFASGllagadggigs 206 :::: :::::::: d1v8aa_ 191 tgafvavteplkatTSALvtfgiaaekayeeakypgsfhvkLYDWLYRI----------- 239 d1hl2a_ 207 tynimgwryqgivkalkegdiqtaqklqtecnkvidlliktgvfrglktvlhymdvvsvp 266 d1v8aa_ 240 ------------------------------------------------------------ 240 d1hl2a_ 267 lcrkpfgpvdekylpelkalaqqlmqerg 295 d1v8aa_ 240 --------------nenvirtyakvreve 254 FAST alignment (Normalized score: 3.21 Raw score:879.60) d1hl2a_ 1 TNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQV 60 d1v8aa_ 1 ------------------------------------------------------------ 1 d1hl2a_ 61 LEIVAEEAKG-------------KIKLIAHVG----------------------CVSTAE 85 :::::::: :::::: d1v8aa_ 1 ----------MKFIIEALKRVRERRPLVHNI-TNFVVMNTTANALLALGASPVMAHAEEE 49 d1hl2a_ 86 SQQLAASAKRYGFDAVSAVTPFYYPF--------SFEEHCDHYRAIIDSADGLPMVVYNI 137 :::::: ::::::: :::::::::::::: ::::::::: d1v8aa_ 50 LEEMIR-----LADAVVI--------NIGTLDSGWRRSMVKATEIANE--LGKPIVLDP- 93 d1hl2a_ 138 PARSGVKL--------TLDQINTLVTLPGVGALKQTSG-----------------DLYQM 172 ::::::::: ::::::::: ::::: d1v8aa_ 94 --------VGAGATKFRTRVSLEIL-SRGVDVLKG---NFGEISALLGEEGGEEEAKKLT 141 d1hl2a_ 173 EQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQK 232 :::::: :::::::: d1v8aa_ 142 MNAARE-FNTTVAVT--------------------------------------------- 155 d1hl2a_ 233 ---------------------------------------------------LQTECNKVI 241 ::::::::: d1v8aa_ 156 GAVDYVSDGRRTFAVYNGHELLGRVTGTGCMVAALTGAFVAVTEPLKATTSALVTFGIAA 215 d1hl2a_ 242 DLLIKT------GVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQERG 295 ::::: ::::::::::: d1v8aa_ 216 EKAYE-EAKYPGSFHVKLYDWLY------------------------------------- 237 d1hl2a_ 296 ----------------- 296 d1v8aa_ 238 RINENVIRTYAKVREVE 254 TMalign alignment (TM-score: 0.40 Raw score:118.49) d1hl2a_ 1 --TNLRGV---MAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQ--- 52 :: ::::::::::::::::::::::: d1v8aa_ 1 MK----FIIEA-----------------------LKRVRERRPLVHNITNFVVMNTTANA 33 d1hl2a_ 53 --------SLSEREQ--VL-EIVAEEAKGKIKLIAHVG-CVSTAESQQLAASAKRY--G- 97 ::::: :: :::::: : :::::: ::::::::::::::::: : d1v8aa_ 34 LLALGASP--VMAHAEEELEEMIRLA-D----AVVINIGTLDSGWRRSMVKATEIANELG 86 d1hl2a_ 98 FDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPARSGVKLTLDQINTLVTLP 157 :::::::::: :::: ::::::::::: :::::::::: :::: ::::::: d1v8aa_ 87 KPIVLDPVGA-GATK--FRTRVSLEILS---RGVDVLKGNF-----GEIS-ALLGEEG-- 132 d1hl2a_ 158 GVGALKQTSGDLYQMEQIRREHPD---LVLYNGYDEIFASGLL---AGADGG-------- 203 :::::::::::::: ::::::: ::: ::: ::::: d1v8aa_ 133 ----------GEEEAKKLTMNAAREFNTTVAVTG-AVD--YVSDGR-RTFAVYNGHELLG 178 d1hl2a_ 204 -----I--GSTYN--IMG------WRYQG-IVK--ALKEGDIQTAQKLQTECNKVIDL-L 244 : ::::: : ::: :: : ::::::::::: : d1v8aa_ 179 RVTGTGCMVAALTGA--FVAVTEP--LKAT-TSAL---------V--TFGIAAEKAYEEA 222 d1hl2a_ 245 IK--TGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQER-------- 294 :: ::: ::::::: : : :::::: d1v8aa_ 223 KYPGSFH-VKLYDWL--Y--------------------------R-INENVIRTYAKVRE 252 d1hl2a_ 295 --G 295 d1v8aa_ 253 VE- 254 HHsearch alignment (Probability: 0.04 E-value:0.14) d1hl2a_ 111 FSFEEHCDHYR--AIIDSADGLPMVVYNIPARSG-VKLTLDQINTLVTL----------- 156 ::::::::::: :::::: ::::::: ::::: :::::::::::::: d1v8aa_ 67 LDSGWRRSMVKATEIANEL-GKPIVLD--PVGAGATKFRTRVSLEILSRGVDVLKGNFGE 123 d1hl2a_ 157 -PGVGALKQTSGDL-YQMEQIRREHPDLVLYNGYDEIFASG-----LLAGAD--GGIGST 207 ::::::::::::: :::::::::::::::::::::::::: :::::: :::::: d1v8aa_ 124 ISALLGEEGGEEEAKKLTMNAAREFNTTVAVTGAVDYVSDGRRTFAVYNGHELLGRVTGT 183 d1hl2a_ 208 YNIMGWRYQ 216 ::::::::: d1v8aa_ 184 GCMVAALTG 192