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 <-- 1.647 --> Intermediate <-- 1.333 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1kwga2) through the intermediate protein (d1d3ga_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1d3ga_ Dihydroorotate dehydrogenaseFMN-​linked oxidoreductasesTIM beta/​alpha-​barrelα/β
Hit d1kwga2 A4 beta-​galactosidase(Trans)glycosidasesTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 1.647 --> Intermediate
DALI alignment (Z-score: 7.2 Raw score:865.90) query 1 mietpyyLIDKAK-----------------------------------ltrnmeriahvr 25 :::::: d1d3ga_ 1 -------MATGDErfyaehlmptlqglldpesahrlavrftslgllpfqdsdmlevrvlg 53 query 26 eksgaKALLALKcfatwsvfDLMRD-YMDGTTSSSL------------------------ 60 ::::::: ::::: :::::::::: d1d3ga_ 54 hkfrnPVGIAAGfdkhgeavDGLYKmGFGFVEIGSVtpkpqegnprprvfrlpedqavin 113 query 61 ----------------fevrlgRERFG---KETHAYSVA---------YGDNEIDEVVSH 92 ::::: ::::::::: :::::::::::: d1d3ga_ 114 rygfnshglsvvehrlrarqqkQAKLTedgLPLGVNLGKnktsvdaaeDYAEGVRVLGPL 173 query 93 ADKIIFNS-------------ISQLERFADKAA------GIARGLRLNPQrlgewDVPKV 133 :::::::: :::::::::::: ::::::::::: ::::: d1d3ga_ 174 ADYLVVNVsspntaglgkaelRRLLTKVLQERDglrrvhRPAVLVKIAPD-ltsqDKEDI 232 query 134 ERVM--DRINGFMIHNN-------------------CENKdfglFDRMLGEIEErFGALI 172 :::: ::::::::::: :::: :::::::::: ::::: d1d3ga_ 233 ASVVkeLGIDGLIVTNTtvsrpaglqgalrsetgglSGKP---lRDLSTQTIREmYALTQ 289 query 173 ARVdWVSLGGGIHFtgddypvdAFSARLRAFSdrygvqIYLEPGEASITKSttlevtvld 232 ::: :::::::::: :::::::::: ::::::::::::: d1d3ga_ 290 GRV-PIIGVGGVSS-------gQDALEKIRAG-----aSLVQLYTALTFWG--------- 327 query 233 tlynknlaivdssieahmldlliyretakvlpnegshsymicgksclagdvfgefrfaee 292 d1d3ga_ 328 ------------------------------------------------------------ 328 query 293 lkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1d3ga_ 328 -----------------------ppvvgkvkreleallkeqgfggvtdaigadhrr 360 FAST alignment (Normalized score: 4.17 Raw score:1474.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGA------------------------------ 30 d1d3ga_ 1 ------------------------------MATGDERFYAEHLMPTLQGLLDPESAHRLA 30 query 31 ----------------------------KALLALKCFA--TWSVFDLMR-DYMDGTTSS- 58 :::::::: ::::::::: ::::::: d1d3ga_ 31 VRFTSLGLLPFQDSDMLEVRVLGHKFRNPVGIAAGF--DKHGEAVDGLYKMGFGFVE--I 86 query 59 -----------------------------------SLFEVRLGRERFG------------ 71 :::::::::: d1d3ga_ 87 GSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRA---RQQKQAKLTEDG 143 query 72 KETHAYSVAY------------GDNEIDEVVSHADKIIFN--------------SISQLE 105 ::::::: ::::::::::::::::: :::::: d1d3ga_ 144 LPLGVNL---GKNKTSVDAAEDYAEGVRVLGPLADYLVV-NVSSPNTAGLGKAELRRLLT 199 query 106 RFADKAA------GIARGLRLNPQRLGEW---------DVPKVERVMD-RINGFMIHNNC 149 ::::::: :::::::::: ::::::: :::::: d1d3ga_ 200 KVLQERDGLRRVHRPAVLVKIAP------DLTSQDKEDIASVVKE---LGIDGLI----- 245 query 150 ENK---------------------------DFGLFDRMLGEIEERFGALIARV----DWV 178 ::::::::::::::: ::: d1d3ga_ 246 ---VTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYAL--------TQGRVPI 294 query 179 SLGGGIHFTGDDYPVDA-FSARLRAFSDRYGVQ--IYLEPGEASITKSTTLEVTVLDTLY 235 :::::: ::::::::::: ::::::::: d1d3ga_ 295 IGVGGV-----------SSGQDALEKIRA----GASLVQLYTAL---------------- 323 query 236 NKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKV 295 d1d3ga_ 324 ------------------------------------------------------------ 324 query 296 GDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS------- 348 d1d3ga_ 324 -----------------------------------------------------TFWGPPV 330 query 349 ------------------------------ 349 d1d3ga_ 331 VGKVKRELEALLKEQGFGGVTDAIGADHRR 360 TMalign alignment (TM-score: 0.36 Raw score:123.76) query 1 ---------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWS-------- 43 :: d1d3ga_ 1 MATGDERFY-----------------------------------------AEHLMPTLQG 19 query 44 -------VFDLMRDYMDGTTSSSLFE--VR----L-GRE---------------RFGKET 74 ::::: : : :: :::: d1d3ga_ 20 LLDPESA--------------HRLAVRF-TSLGLLP-FQDSDMLEVRVLGHKFR--NPVG 61 query 75 HAY--SVAYGDNEIDEVVSH-A-DKIIF-N------------------------------ 99 ::: ::::: :::::::: : ::::: : d1d3ga_ 62 IAAGFDKHGE--AVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNS 119 query 100 --SISQLERFA-D--KAA-G----IARGLRLNPQR-L--G-EWDVPKVERVMDRINGFMI 145 ::::::::: : ::: : ::::::::::: : : ::::::::::::::::::: d1d3ga_ 120 HGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVV 179 query 146 HNNCEN---KDFGLFDRMLGEIEERFGALIA------RVDWVSLGGGIHFTGDDYPVDAF 196 :::::: :::::::::::::::::: ::::::::: ::: ::: :: d1d3ga_ 180 NVSSPNTAG----LGKAELRRLLTKVLQERDGLRRVHRPAVLVKIA-PDL----TSQ-DK 229 query 197 SARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIY 256 :::::::::::::::::::::: ::::::: :::::: : d1d3ga_ 230 EDIASVVKELGIDGLIVTNTTV-SRPAGLQ---------------------GALRSE--T 265 query 257 RETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMV------ 310 : :::::: d1d3ga_ 266 -G----------------------------------------------GLSGKPLRDLST 278 query 311 ------------------------------------------------------------ 311 d1d3ga_ 279 QTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKREL 338 query 311 ----------------------KKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1d3ga_ 339 EALLKEQGFGGVTDAIGADHRR-------------------------------------- 360 HHsearch alignment (Probability: 0.13 E-value:0.02) query 98 FNSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDR-INGFMI----------- 145 :::::::::::::::::::::::::::::::::::::::::: :::::: d1d3ga_ 198 LTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGL 257 query 146 -----HNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGG 182 ::::::::::::::::::::::::::::::::::::: d1d3ga_ 258 QGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGG 299
Intermediate <-- 1.333 --> Hit
DALI alignment (Z-score: 12.2 Raw score:1485.80) d1d3ga_ 1 matgderfyaehlmptlqglldpesahrlavrftslgllpfqdsdmlevrvlghkfrnPV 60 :: d1kwga2 1 ----------------------------------------------------------ML 2 d1d3ga_ 61 GIAagFDKH-------geAVDGLYKMGFGFVEIGSVTPkpqegnprprvfrlpedqavin 113 ::: :::: :::::::::::::::::::: d1kwga2 3 GVC--YYPEhwpkerwkeDARRMREAGLSHVRIGEFAW---------------------- 38 d1d3ga_ 114 rygfnsHGLS-----vvEHRLRARQQKQAKLTedgLPLGVNLG--KNKT----------- 155 :::: ::::::::::::::: :::::::: :::: d1kwga2 39 ------ALLEpepgrleWGWLDEAIATLAAEG---LKVVLGTPtaTPPKwlvdrypeilp 89 d1d3ga_ 156 -----------------------sVDAAEDYAEGVRVLGPL--ADYLVVNVSspNTAG-- 188 ::::::::::::::::: ::::::::: :::: d1kwga2 90 vdregrrrrfggrrhycfsspvyrEEARRIVTLLAERYGGLeaVAGFQTDNEygCHDTvr 149 d1d3ga_ 189 ------------------------------------------------------------ 189 d1kwga2 150 cycprcqeafrgwlearygtiealneawgtafwsqryrsfaevelphltvaepnpshlld 209 d1d3ga_ 189 ---lGKAELRRLLTKVLQERDGLrrvHRPAVLVKIAPDlTSQDkeDIASVVKelGIDGLI 245 ::::::::::::::::::: :::::::::::: :::: ::::::: :::::: d1kwga2 210 yyrfASDQVRAFNRLQVEILRAH--aPGKFVTHNFMGF-FTDL--DAFALAQ--DLDFAS 262 d1d3ga_ 246 VTNT--TVSRPAGLQGALRSetgglsgkPLRDLsTQTIREMYALtqgRVPIIG-VGGV-- 300 :::: :::::::::::::: ::::: :::::::::: :::::: :::: d1kwga2 263 WDSYplGFTDLMPLPPEEKL--ryartgHPDVA-AFHHDLYRGV--gRGRFWVmEQQPgp 317 d1d3ga_ 301 -------------sSGQDALEKIRAGASLVQLY-------------TALT------FWGP 328 ::::::::::::::::::: :::: :::: d1kwga2 318 vnwaphnpspapgmVRLWTWEALAHGAEVVSYFrwrqapfaqeqmhAGLHrpdsapDQGF 377 d1d3ga_ 329 PVVGKVKRELEAllkeqgfgGVTDaigadhrr 360 :::::::::::: :::: d1kwga2 378 FEAKRVAEELAA--------LALP-------- 393 FAST alignment (Normalized score: 6.07 Raw score:2285.00) d1d3ga_ 1 MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDMLEVRVLGHKFRNPV 60 :: d1kwga2 1 ----------------------------------------------------------ML 2 d1d3ga_ 61 GIAAGFDKHGE------------AVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPED 108 :::: :::::::::::::::: d1kwga2 3 GVCY-------YPEHWPKERWKEDARRMREAGLSHVRIG--------------------- 34 d1d3ga_ 109 QAVINRYGFNSHGLSV--------------VEHRLRARQQKQAKLTEDGLPLGVNL---G 151 :::::::::::::: ::::::::: : d1kwga2 35 ----------------EFAWALLEPEPGRLEWGWLDEAIATLAA---EGLKVVLGTPTAT 75 d1d3ga_ 152 KNKTSV-----------------------------------DAAEDYAEGVRVLG--PLA 174 :::: :::::::::::::: ::: d1kwga2 76 PPKW--LVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVTLLAERYGGLEAV 133 d1d3ga_ 175 DYLVVNVSSPNTAGL--------------------------------------------- 189 :::: d1kwga2 134 AGFQ-----------TDNEYGCHDTVRCYCPRCQEAFRGWLEARYGTIEALNEAWGTAFW 182 d1d3ga_ 190 -------------------------------GKAELRRLLTKVLQERDGLRRVH----RP 214 ::::::::::::::::: :: d1kwga2 183 SQRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQVRAFNRLQVEILR------AHAPGK 236 d1d3ga_ 215 AVLVKIAPDLTSQDKE----DIASVVKEL-GIDGLIVTNTT----------VSRPAGLQG 259 ::::::::: :::::: :::::: ::::: d1kwga2 237 FVTHNFMGF-------FTDLDAFALA---QDLDFAS-----WDSYPLGFTDLMPLP---- 277 d1d3ga_ 260 ALRSETGGLSGKP-----------LRDLSTQTIREMYALTQGRVPIIGVGGVS------- 301 ::::::::::::::::: :::::: d1kwga2 278 -------------PEEKLRYARTGHPDVAAFHHDLYRGVGR--GRFWVM----EQQPGPV 318 d1d3ga_ 302 -------------SGQDALEKIRAGASLVQLYTALTFW---------------------- 326 ::::::::::::::::: d1kwga2 319 NWAPHNPSPAPGMVRLWTWEALAHGAEVVS--------YFRWRQAPFAQEQMHAGLHRPD 370 d1d3ga_ 327 -----GPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR---- 360 :::::::::::::: d1kwga2 371 SAPDQGFFEAKRVAEELAA--------------------LALP 393 TMalign alignment (TM-score: 0.43 Raw score:156.07) d1d3ga_ 1 -----------MATGDERFYAE----------------------HLMPTLQGLLDPESAH 27 :: : d1kwga2 1 MLGVCYYPEHW---------PKERWKEDARRMREAGLSHVRIGE---------------F 36 d1d3ga_ 28 RLAVRFTSLGLLP----FQ-DSDMLEVRVLGHKFRNPVGIAA-GFD-------------- 67 ::::::::::::: :: :::::::: : ::::::: ::: d1kwga2 37 AWALLEPEPGRLEWGWLDEAIATLAAEG-----L-KVVLGTPTATPPKWLVDRYPEILPV 90 d1d3ga_ 68 ------------K-H-------G--E--AVDGLYKMGF----G-FVE-IGSVTP-KPQEG 96 : : : : :::::::::: : ::: :::::: ::::: d1kwga2 91 DREGRRRRFGGRRHYCFSSPVYREEARRIVTLLAERYGGLEAVAGFQTDNEYGCHDTVRC 150 d1d3ga_ 97 ------------------------------------------------------------ 97 d1kwga2 151 YCPRCQEAFRGWLEARYGTIEALNEAWGTAFWSQRYRSFAEVELPHLTVAEPNPSHLLDY 210 d1d3ga_ 97 --NPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNK 154 :::::::::::::::::::::::: :::::::: d1kwga2 211 YR-----------------------FASDQVRAFNRLQVEILRAHAPGK-FVTHNFMG-- 244 d1d3ga_ 155 TSVDAAEDYAEGVRVLGPLADYLVVNVSSPNT-AGL--------------GKAELRRLLT 199 : :::::: ::::::::::::::::::: ::: :::::::::: d1kwga2 245 ----F-FTDLDA-FALAQDLDFASWDSYPLGFTDLMPLPPEEKLRYARTGHPDVAAFHHD 298 d1d3ga_ 200 KVLQERDGLRRVHRPAVLVKIAPD----------LTSQDKEDIASVVKELGIDGLIVTNT 249 ::::::: ::::::::::: :::::::::::::::::::::::::: d1kwga2 299 LYRGVGR------GRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVSYFRW 352 d1d3ga_ 250 TVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALT-QGRV----PIIGVGGVSSGQ 304 : :: : : :: ::::::::::::::::::::::::: :::: d1kwga2 353 R-QA---P-F-AQ-EQMHAGLHRPDSAPDQGFFEAKRVAEELAALALP------------ 393 d1d3ga_ 305 DALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR 360 d1kwga2 394 -------------------------------------------------------- 394 HHsearch alignment (Probability: 0.10 E-value:0.23) d1d3ga_ 198 LTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGL 257 :::::::::: :::::::::::::::::::::::::: :: :::::::::::::: d1kwga2 222 NRLQVEILRA--HAPGKFVTHNFMGFFTDLDAFALAQD-----LD-FASWDSYPLGFTDL 273 d1d3ga_ 258 QGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGV---GGVS----S-------- 302 :: ::::::::::::::::::::::::::::::::::::: :::: : d1kwga2 274 MP-LPPEEKLRYARTGHPDVAAFHHDLYRGVGRGRFWVMEQQPGPVNWAPHNPSPAPGMV 332 d1d3ga_ 303 GQDALEKIRAGASLVQLYT 321 ::::::::::::::::::: d1kwga2 333 RLWTWEALAHGAEVVSYFR 351