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 <-- 1.586 --> Intermediate <-- 1.252 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1dqua_) through the intermediate protein (d1i4na_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1i4na_ Indole-​3-​glycerophosphate synthase,​ IPGSRibulose-​phoshate binding barrelTIM beta/​alpha-​barrelα/β
Hit d1dqua_ Isocitrate lyasePhosphoenolpyruvate/​pyruvate domainTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 1.586 --> Intermediate
DALI alignment (Z-score: 10.4 Raw score:1010.00) query 1 -----------mietpyylidkakltrnmeriahvrekSGAKALLALKC----------f 39 ::::::::::: d1i4na_ 1 rrlweiveakkkdileidgenlivqrrnhrflevlsgkERVKIIAEFKKaspsagdinad 60 query 40 aTWSV-FDLMRDYMDGTTSSS--------LFEVRLGRERFGKETHAYSVAYGDNEIDEVV 90 :::: ::::::::::::::: ::::::::::::::::::::::::::::::: d1i4na_ 61 aSLEDfIRMYDELADAISILTekhyfkgdPAFVRAARNLTCRPILAKDFYIDTVQVKLAS 120 query 91 S-HADKIIFNS----ISQLERFADKAA--GIARGLRLNPQrlgEWDVpkVERVMdrINGF 143 : ::::::::: :::::::::::: ::::::::::: :::: ::::: :::: d1i4na_ 121 SvGADAILIIAriltAEQIKEIYEAAEelGMDSLVEVHSR--eDLEK-vFSVIR--PKII 175 query 144 MIHNNcenkdfglFDRMLGEIEERFgalIARVdWVSLGGGIHFTgddypvdAFSARLRAF 203 ::::: :::::::::::: :::: ::::::::::: ::::::::: d1i4na_ 176 GINTR-dldtfeiKKNVLWELLPLV---PDDT-VVVAESGIKDP-------RELKDLRGK 223 query 204 SdrygvqIYLEPGEASITKSTtlevtvldtlynknlaivdssieahmldlliyretakvl 263 : :::::::::::::: d1i4na_ 224 V------NAVLVGTSIMKAEN--------------------------------------- 238 query 264 pnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpai 323 d1i4na_ 239 ------------------------------------------------------------ 239 query 324 aireldgsvrtvreftyadyeqsls 348 d1i4na_ 239 ------------prrfleemrawse 251 FAST alignment (Normalized score: 5.64 Raw score:1667.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS-------------------------------- 28 d1i4na_ 1 ----------------------------RRLWEIVEAKKKDILEIDGENLIVQRRNHRFL 32 query 29 -------GAKALLALKCFATWS------------------VFDLMRDYMDGTTS------ 57 :::::::: :::::::::::::: d1i4na_ 33 EVLSGKERVKIIAEF-------KKASPSAGDINADASLEDFIRMYDELADAISILTEKHY 85 query 58 --SSLFEVRLGRERFGKETHAYSVA--YGDNEIDEVVS-HADKIIF----NSISQLERFA 108 ::::::::::::::::::::: ::::::::::: ::::::: :::::::::: d1i4na_ 86 FKGDPAFVRAARNLTCRPILAKD--FYIDTVQVKLASSVGADAILIIARILTAEQIKEIY 143 query 109 DKA--AGIARGLRLNPQRLGEW----DVPKVERVMD--RINGFMIHNNCENKDFGL---- 156 ::: ::::::::: ::::::: :::::::: d1i4na_ 144 EAAEELGMDSLVEV--------HSREDLEKVFS---VIRPKIIGIN----------TRDL 182 query 157 -----FDRMLGEIEERFGALIARV----DWVSLGGGIHFTGDDYPVDAFSARLRAFSDRY 207 ::::::::::: :::::::::: :::::::::: d1i4na_ 183 DTFEIKKNVLWELLPL--------VPDDTVVVAESGIK-------DPRELKDLRG----- 222 query 208 GVQ--IYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPN 265 ::::::::: d1i4na_ 223 ---KVNAVLVGTSI---------------------------------------------- 233 query 266 EGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAI 325 d1i4na_ 234 ------------------------------------------------------------ 234 query 326 RELDGSVRTVREFTYADYEQSLS------------------ 348 d1i4na_ 234 -----------------------MKAENPRRFLEEMRAWSE 251 TMalign alignment (TM-score: 0.41 Raw score:143.58) query 1 ----------------------------------------------------------MI 2 d1i4na_ 1 RRLWEIVEAKKKDILEIDGENLIVQRRNHRFLEVLSGKERVKIIAEFKKASPSAGDIN-- 58 query 3 ETPYYLIDKAKLTRNMERIAHVREKSGAKALLALK---CFATWSVFDLMRDYM---DGTT 56 :::::::::::::: :::::::::: ::::::::::::::: :::: d1i4na_ 59 ----------ADASLEDFIRMYDE-LADAISILTEKHYFKGDPAFVRAARNLTCRPILAK 107 query 57 SSSLF-EVRLGRERFGKETHAYS-VAYGDNEIDEVVS-H-----ADKIIFNSISQLERFA 108 ::::: ::::::::::::::::: ::::::::::::: : :::::::::::::::: d1i4na_ 108 DFYIDTVQVKLASSVGADAILIIARILTAEQIKEIYEAAEELGMDSLVEVHSREDLEKVF 167 query 109 DKAAGIARGLRLNP---QRLGEWDVPKVERVMDR-INGFMIHNNCENKDFGLFDRMLGEI 164 :::::::::::::: ::::::::::::::::: ::::::::: : : :: : d1i4na_ 168 SVIRPKIIGINTRDLDTFEIKKNVLWELLPLVPDDTVVVAESGI--------K-D-PR-E 216 query 165 EERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEASITKST 224 :: :: ::::::::: ::::: : ::::::::::::::: : d1i4na_ 217 LK--DL-RGKVNAVLV-GTSIM-K-AENPRRFLEEMRAWS-E------------------ 251 query 225 TLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVF 284 d1i4na_ 252 ------------------------------------------------------------ 252 query 285 GEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYE 344 d1i4na_ 252 ------------------------------------------------------------ 252 query 345 QSLS 348 d1i4na_ 252 ---- 252 HHsearch alignment (Probability: 0.22 E-value:0.02) query 57 SSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFN------SISQLERFADK 110 ::::::::::::::::::::::::::::::::::::::::::: ::::::::::: d1i4na_ 110 YIDTVQVKLASSVGADAILIIARILTAEQIKEIYEAAEELGMDSLVEVHSREDLEKVFSV 169 query 111 AAGIARGLRLNPQRLGEWDVPKVERVMDRI-NGFMIHNNCENKDFGLFDRM 160 :::::::::::::::::::::::::::::: :::::::::::::::::::: d1i4na_ 170 IRPKIIGINTRDLDTFEIKKNVLWELLPLVPDDTVVVAESGIKDPRELKDL 220
Intermediate <-- 1.252 --> Hit
DALI alignment (Z-score: 13.2 Raw score:1432.30) d1i4na_ 1 -------------------------rrlweiveakkkdileidgeNLIVQRRN--HRFLE 33 :::::::: ::::: d1dqua_ 1 syieeedqrywdevaavknwwkdsrwrytkrpftaeqivakrgnlKIEYPSNVqaKKLWG 60 d1i4na_ 34 VLS--GKER-VKIIAEFKkaspsagdinadasLEDFIRMYDELADAISILTEkhYFKG-- 88 ::: :::: :::::::: :::::::::::::::::::: :::: d1dqua_ 61 ILErnFKNKeASFTYGCL--------------DPTMVTQMAKYLDTVYVSGWqsSSTAss 106 d1i4na_ 89 ---------------DPAFVRAARNL---------------------------TCRPILA 106 ::::::::::: ::::::: d1dqua_ 107 tdepspdladypmntVPNKVNHLWMAqlfhdrkqreermttpkdqrhkvanvdYLRPIIA 166 d1i4na_ 107 KDFYI------DTVQVKLASSVGADAILIIAR--------ILTAEQIKEIYEAAEE---- 148 ::::: ::::::::::::::::::::: :::::::::::::::: d1dqua_ 167 DADTGhggltaVMKLTKLFVERGAAGIHIEDQapgtkgkvLVPISEHINRLVAIRAqadi 226 d1i4na_ 149 --LGMDSLVEVH------------------------------------------------ 158 :::::::::: d1dqua_ 227 mgTDLLAIARTDseaatlitstidhrdhpfiigstnpdiqplndlmvmaeqagkngaelq 286 d1i4na_ 159 ------------------------------------------------------------ 159 d1dqua_ 287 aiedewlakaglklfndavvdainnsplpnkkaaiekyltqskgksnlearaiakeiagt 346 d1i4na_ 159 ---------------------SREDLEKVFSVIR-PKIIGINTRdldtfeIKKN-VLWEL 195 ::::::::::::: ::::::::: :::: ::::: d1dqua_ 347 diyfdweaprtregyyryqggTQCAINRAVAYAPfADLIWMESK------LPDYkQAKEF 400 d1i4na_ 196 LPLV---PDDTVVVAESGIK-----------DPRELKDLRGK-VNAVLVGTSIM-KAEN- 238 :::: ::::::::::::: ::::::::::: ::::::::::: :::: d1dqua_ 401 ADGVhavWPEQKLAYNLSPSfnwkkamprdeQETYIKRLGALgYAWQFITLAGLhTTALi 460 d1i4na_ 239 ----------------------------------------prrfleemrawse 251 d1dqua_ 461 sdtfakayakqgmraygelvqepemangvdvvthqkwsganyvdnmlkmitgg 513 FAST alignment (Normalized score: 6.89 Raw score:2471.00) d1i4na_ 1 RRLWEIVEAKKKDILEIDGENLIVQRRN-------------------------------- 28 d1dqua_ 1 ----------------------------SYIEEEDQRYWDEVAAVKNWWKDSRWRYTKRP 32 d1i4na_ 29 -----------------------HRFLEVLSGK-----ERVKIIAEFKKASPSAGDINAD 60 :::::::: ::::::::: d1dqua_ 33 FTAEQIVAKRGNLKIEYPSNVQAKKLWGILE--RNFKNKEASFTYGC------------- 77 d1i4na_ 61 AS-LEDFIRMYDELADAISILTEKHYFKG-------------------------DPAFVR 94 :::::::::::::::::: :::::: d1dqua_ 78 --LDPTMVTQMAKYLDTVYVS--------GWQSSSTASSTDEPSPDLADYPMNTVPNKVN 127 d1i4na_ 95 AARNL---------------------------TCRPILAKDFYI---------DTVQVKL 118 ::::: ::::::::: ::::::: d1dqua_ 128 HLWMAQLFHDRKQREERMTTPKDQRHKVANVDYLRPIIADA---DTGHGGLTAVMKLTKL 184 d1i4na_ 119 ASSVGADAILIIAR---------ILTAEQIKEIYEAAEE------LGMDSLVEVH----- 158 ::::::::::::: :::::::::::::::: ::::::::: d1dqua_ 185 FVERGAAGIHIED-QAPGTKGKVLVPISEHINRLVAIRAQADIMGTDLLAIART-DSEAA 242 d1i4na_ 159 ------------------------------------------------------------ 159 d1dqua_ 243 TLITSTIDHRDHPFIIGSTNPDIQPLNDLMVMAEQAGKNGAELQAIEDEWLAKAGLKLFN 302 d1i4na_ 159 ------------------------------------------------------------ 159 d1dqua_ 303 DAVVDAINNSPLPNKKAAIEKYLTQSKGKSNLEARAIAKEIAGTDIYFDWEAPRTREGYY 362 d1i4na_ 159 -----SREDLEKVFSVI---RPKIIGINTRDLDT-FEIKKNVLWELLPLV----PDDTVV 205 :::::::::: :::::::: :::::::::::::: :::::: d1dqua_ 363 RYQGGTQCAINRAVA--YAPFADLIWME------SKLPDYKQAKEFADG-VHAVWPEQKL 413 d1i4na_ 206 VAESGIK---------------DPRELKDLRG-KVNAVLVGTSIMKAENPRRFLEEMRAW 249 ::: :::::::::: ::::::::::::: d1dqua_ 414 AYN----LSPSFNWKKAMPRDEQETYIKRLGALGYAWQFITLAGLH-------------- 455 d1i4na_ 250 SE---------------------------------------------------------- 251 d1dqua_ 456 --TTALISDTFAKAYAKQGMRAYGELVQEPEMANGVDVVTHQKWSGANYVDNMLKMITGG 513 TMalign alignment (TM-score: 0.65 Raw score:163.52) d1i4na_ 1 ------------------------------------------RRLWEIVEAKKKDILEID 18 d1dqua_ 1 SYIEEEDQRYWDEVAAVKNWWKDSRWRYTKRPFTAEQIVAKR------------------ 42 d1i4na_ 19 GE---NLIVQR-R--NHRFLEVLS-GK-E-RVKIIAEFKKASPSAGDINADASLEDFIRM 69 : :::: : ::::::::: :: : ::::::::: ::::::: d1dqua_ 43 -GNLK--IEYPSNVQAKKLWGILERNFKNKEASFTYGCL--------------DPTMVTQ 85 d1i4na_ 70 YDELADAISILTEKHYFKG----------------D-PAFVRAARN-L------------ 99 ::::::::::::::::::: : ::::::::: : d1dqua_ 86 MAKYLDTVYVSGWQSSSTASSTDEPSPDLADYPMNTVPNKVNHLWMAQLFHDRKQREERM 145 d1i4na_ 100 --------------TCRPILAKDFYI------DTVQVKLASSVGADAILIIARI------ 133 :::::::::::: :::::::::::::::::::::: d1dqua_ 146 TTPKDQRHKVANVDYLRPIIADADTGHGGLTAVMKLTKLFVERGAAGIHIEDQAPGTKGK 205 d1i4na_ 134 --LT-AE--QIKEIYEAAEE---LGMDSLVEVHS-------------------------- 159 :: :: ::::::::::: ::::::::::: d1dqua_ 206 VLVPISEHINRLVAIRAQADIMGTDLLAIARTDSEAATLITSTIDHRDHPFIIGSTNPDI 265 d1i4na_ 160 ------------------------------------------------------------ 160 d1dqua_ 266 QPLNDLMVMAEQAGKNGAELQAIEDEWLAKAGLKLFNDAVVDAINNSPLPNKKAAIEKYL 325 d1i4na_ 160 -------------------------------------------REDLEKVFSVIR-PKII 175 :::::::::::: :::: d1dqua_ 326 TQSKGKSNLEARAIAKEIAGTDIYFDWEAPRTREGYYRYQGGTQCAINRAVAYAPFADLI 385 d1i4na_ 176 GINTRDLDTFEIKK-NVLWELLPLVP---DDTVVVAESGI---KD-------PR-ELKDL 220 ::::: ::: ::::::::::: ::::::::::: :: :: ::::: d1dqua_ 386 WMESK------LPDYKQAKEFADGVHAVWPEQKLAYNLSPSFNWKKAMPRDEQETYIKRL 439 d1i4na_ 221 RGK-VNAVLVGTSIMKA--EN--------------------------------------- 238 ::: ::::::::::::: :: d1dqua_ 440 GALGYAWQFITLAGLHTTALISDTFAKAYAKQGMRAYGELVQEPEMANGVDVVTHQKWSG 499 d1i4na_ 239 --------------PRRFLEEMRAWSE 251 d1dqua_ 500 ANYVDNMLKMITGG------------- 513 HHsearch alignment (Probability: 0.07 E-value:0.07) d1i4na_ 147 EELGMDSLVEVHSREDLEKVFS-----VIRPKIIGINTRDLDTFEIKKN 190 :::::::::::::::::::::: :::::::::::::::::::::: d1dqua_ 225 DIMGTDLLAIARTDSEAATLITSTIDHRDHPFIIGSTNPDIQPLNDLMV 273