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 <-- 1.714 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1ofda2) 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 d1ofda2 Alpha subunit of glutamate synthase,​ central and FMN domainsFMN-​linked oxidoreductasesTIM 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 <-- 1.714 --> Hit
DALI alignment (Z-score: 15.7 Raw score:1860.50) d1d3ga_ 1 ------------------------------------------------------------ 1 d1ofda2 1 faektlfndaqtvlqqqaafgytaedvemvvvpmasqgkeptfcmgddtplavlshkprl 60 d1d3ga_ 1 ------------------------------------------------------------ 1 d1ofda2 61 lydyfkqrfaqvtnppidplrenlvmslamflgkrgnllepkaesartiklrsplvneve 120 d1d3ga_ 1 ------------------------------------------------------------ 1 d1ofda2 121 lqaiktgqlqvaevstlydldgvnsledaltnlvktaiatvqagaeilvltdrpngailt 180 d1d3ga_ 1 ------------------------------------------------------------ 1 d1ofda2 181 enqsfippllavgavhhhliraglrlkaslivdtaqcwsthhfaclvgygasaicpylal 240 d1d3ga_ 1 ------------------------------------------------------------ 1 d1ofda2 241 esvrqwwldektqklmengrldridlptalknyrqsveaglfkilskmgisllasyhgaq 300 d1d3ga_ 1 ------------------------------------------------------------ 1 d1ofda2 301 ifeaiglgaelveyafagttsrvggltiadvagevmvfhgmafkklenfgfvnyrpggey 360 d1d3ga_ 1 --matgdERFYAEhLMPT------------lqglldpesahrlavrftslgllpfqDSDM 46 :::::: :::: :::: d1ofda2 361 hmnspemSKSLHK-AVAAydhyelyrqylkdrpvtalrdlldfnadqpaisleeveSVES 419 d1d3ga_ 47 LevrvlghkfRNPVGIAAgFDKH------GEAV-DGLYKMGfGFVEIGSVtpkpqegnpr 99 : :::::::: :::: :::: ::::::: :::::::: d1ofda2 420 I---------VKRFCTGG-MSLGalsreaHETLaIAMNRLG-AKSNSGEG---------- 458 d1d3ga_ 100 prvfrlpedqavinrygfnshglsvVEHRlrARQQK-----------------qaklted 142 :::: ::::: d1ofda2 459 -------------------------GEDV--VRYLTlddvdsegnsptlphlhglqngdt 491 d1d3ga_ 143 glpLGVNLGKNktsvdaaedyaeGVRVLGPLADYLVVNVS----SPNT------------ 186 :::::::: ::::::::::::::::: :::: d1ofda2 492 ansAIKQIASG---------rfgVTPEYLMSGKQLEIKMAqgakPGEGgqlpgkkvseyi 542 d1d3ga_ 187 --------------AGLG-kaELRRLLTKVLQERDGLrrvHRPAVLVKIAPDLtsqDKED 231 :::: :::::::::::::::: ::::::::::::: :::: d1ofda2 543 amlrrskpgvtlisPPPHhdiYSIEDLAQLIYDLHQI--nPEAQVSVKLVAEI---GIGT 597 d1d3ga_ 232 IASVVKELGIDGLIVTNTtvsrpaglqgalrsetggLSGK---------plrdLSTQTIR 282 :::::::::::::::::: :::: ::::::: d1ofda2 598 IAAGVAKANADIIQISGH------------------DGGTgasplssikhagsPWELGVT 639 d1d3ga_ 283 EMYALTQ-----GRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWG---------- 327 ::::::: :::::::::::::::::::::::::::::::::::::: d1ofda2 640 EVHRVLMenqlrDRVLLRADGGLKTGWDVVMAALMGAEEYGFGSIAMIAEgcimarvcht 699 d1d3ga_ 328 -------------------------PPVVGKVKRELEALLKEQGFGGVTDAIGADHRR-- 360 ::::::::::::::::::::::::::::::::: d1ofda2 700 nncpvgvatqqerlrqrfkgvpgqvVNFFYFIAEEVRSLLAHLGYRSLDDIIGRTDLLkv 759 d1d3ga_ 361 ---------------------------------- 361 d1ofda2 760 rsdvqlsktqnltldcllnlpdtkqnrqwlnhep 793 FAST alignment (Normalized score: 6.42 Raw score:3427.00) d1d3ga_ 1 MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQD----------------- 43 d1ofda2 1 -------------------------------------------FAEKTLFNDAQTVLQQQ 17 d1d3ga_ 44 ------------------------------------------------------------ 44 d1ofda2 18 AAFGYTAEDVEMVVVPMASQGKEPTFCMGDDTPLAVLSHKPRLLYDYFKQRFAQVTNPPI 77 d1d3ga_ 44 ------------------------------------------------------------ 44 d1ofda2 78 DPLRENLVMSLAMFLGKRGNLLEPKAESARTIKLRSPLVNEVELQAIKTGQLQVAEVSTL 137 d1d3ga_ 44 ------------------------------------------------------------ 44 d1ofda2 138 YDLDGVNSLEDALTNLVKTAIATVQAGAEILVLTDRPNGAILTENQSFIPPLLAVGAVHH 197 d1d3ga_ 44 ------------------------------------------------------------ 44 d1ofda2 198 HLIRAGLRLKASLIVDTAQCWSTHHFACLVGYGASAICPYLALESVRQWWLDEKTQKLME 257 d1d3ga_ 44 ------------------------------------------------------------ 44 d1ofda2 258 NGRLDRIDLPTALKNYRQSVEAGLFKILSKMGISLLASYHGAQIFEAIGLGAELVEYAFA 317 d1d3ga_ 44 ------------------------------------------------------------ 44 d1ofda2 318 GTTSRVGGLTIADVAGEVMVFHGMAFKKLENFGFVNYRPGGEYHMNSPEMSKSLHKAVAA 377 d1d3ga_ 44 ----------------------------------------SDMLEVRVLGHKFRNPVGIA 63 :::: :::::: d1ofda2 378 YDHYELYRQYLKDRPVTALRDLLDFNADQPAISLEEVESVESIV----------KRFCTG 427 d1d3ga_ 64 AGFD------KHGEAVDGLYKMGF------GFVEIGSVTPKPQEGNPRPRVFRLPEDQAV 111 ::::::::::: :::::: d1ofda2 428 ----GMSLGALSREAHETLAI---AMNRLGAKSNSG------------------------ 456 d1d3ga_ 112 INRYGFNSHGLSVVEHR----LRARQQKQAKLTEDGLP---------------------- 145 ::::: d1ofda2 457 -----------------EGGEDVVRY------------LTLDDVDSEGNSPTLPHLHGLQ 487 d1d3ga_ 146 -------LGVNLGKNKTSVDAAEDYAEG------VRVLGPLADYLVVNVSSPNTAG---- 188 :::::: :::::::::::::::::: d1ofda2 488 NGDTANSAIKQIA---------------SGRFGVTPEYLMSGKQLEIKMAQG----AKPG 528 d1d3ga_ 189 -----------------------------------LGKAELRRLLTKVLQERDGLRRVH- 212 :::::::::::::::: d1ofda2 529 EGGQLPGKKVSEYIAMLRRSKPGVTLISPPPHHDIYSIEDLAQLIYDLHQI--------N 580 d1d3ga_ 213 -RPAVLVKIAPDL---TSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRS----- 263 :::::::::: ::::::::: :::::::: d1ofda2 581 PEAQVSVKLVA--EIGIGTIAAGVA----KANADIIQ------------------ISGHD 616 d1d3ga_ 264 -----------ETGGLSGKPLRD-LSTQTIREMYALTQ-------GRVPIIGVGGVSSGQ 304 :::: :::::::::::: ::::::::::::::: d1ofda2 617 GGTGASPLSSIKHAG--------SPWELGVTEVHRV--LMENQLRDRVLLRADGGLKTGW 666 d1d3ga_ 305 DALEKIRAGASLVQLYTALTFW------------------------------------GP 328 ::::::::::::::::::::: :: d1ofda2 667 DVVMAALMGAEEYGFGSIAMI-AEGCIMARVCHTNNCPVGVATQQERLRQRFKGVPGQVV 725 d1d3ga_ 329 PVVGKVKRELEALLKEQGFGGVTDAIGADHRR---------------------------- 360 ::::::::::::::::::::::::::: d1ofda2 726 NFFYFIAEEVRSLLAHLGYRSLDDIIG-----RTDLLKVRSDVQLSKTQNLTLDCLLNLP 780 d1d3ga_ 361 ------------- 361 d1ofda2 781 DTKQNRQWLNHEP 793 TMalign alignment (TM-score: 0.58 Raw score:210.60) d1d3ga_ 1 ------------------------------------------------------------ 1 d1ofda2 1 FAEKTLFNDAQTVLQQQAAFGYTAEDVEMVVVPMASQGKEPTFCMGDDTPLAVLSHKPRL 60 d1d3ga_ 1 ------------------------------------------------------------ 1 d1ofda2 61 LYDYFKQRFAQVTNPPIDPLRENLVMSLAMFLGKRGNLLEPKAESARTIKLRSPLVNEVE 120 d1d3ga_ 1 ------------------------------------------------------------ 1 d1ofda2 121 LQAIKTGQLQVAEVSTLYDLDGVNSLEDALTNLVKTAIATVQAGAEILVLTDRPNGAILT 180 d1d3ga_ 1 ------------------------------------------------------------ 1 d1ofda2 181 ENQSFIPPLLAVGAVHHHLIRAGLRLKASLIVDTAQCWSTHHFACLVGYGASAICPYLAL 240 d1d3ga_ 1 ------------------------------------------------------------ 1 d1ofda2 241 ESVRQWWLDEKTQKLMENGRLDRIDLPTALKNYRQSVEAGLFKILSKMGISLLASYHGAQ 300 d1d3ga_ 1 ------------------------------------------------------------ 1 d1ofda2 301 IFEAIGLGAELVEYAFAGTTSRVGGLTIADVAGEVMVFHGMAFKKLENFGFVNYRPGGEY 360 d1d3ga_ 1 ------------M--ATGDERFYAE----------------------------HLMPTLQ 18 : :::::::::: d1ofda2 361 HMNSPEMSKSLHKAVAAYDHYELYRQYLKDRPVTALRDLLDFNADQPAISLEE------- 413 d1d3ga_ 19 GLLDPESAHRLAVRFTSLGLLPFQDSDMLEVRVLGHKFRNPVGIAAGFD--K-H--GEAV 73 :::::: :::::::::::: : : :::: d1ofda2 414 -------------------------VESVES------IVKRFCTGGMSLGALSREAHETL 442 d1d3ga_ 74 DGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQ 133 ::::: :::::::::: : : ::::::::: d1ofda2 443 AIAMN-RLGAKSNSGE-----------------------------G--G--EDVVRYLTL 468 d1d3ga_ 134 QK------------------QAKLT-EDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLA 174 :: ::: :::::::::: :: :::::::::: d1ofda2 469 DDVDSEGNSPTLPHLHGLQN--GDTA---NSAIKQIASG--------RF-GVTPEYLMSG 514 d1d3ga_ 175 DYLVVNVSS--P--NT--------------------------AGL---GKAELRRLLTKV 201 ::::::::: : :: ::: :::::::::: d1ofda2 515 KQLEIKMAQGAKPGEGGQLPGKKVSEYIAMLRRSKPGVTLISPPPHHD--IYSIEDLAQL 572 d1d3ga_ 202 LQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTV----SRPAGL 257 ::::::::: :::::::::: ::: ::::::::::::::::::::::: d1ofda2 573 IYDLHQINP--EAQVSVKLVA-EIG--IGTIAAGVAKANADIIQISGHDGGTGA------ 621 d1d3ga_ 258 QGALRSETGGLS-GKPLRDLSTQTIREMYALTQ----GR-VPIIGVGGVSSGQDALEKIR 311 :::::::: : ::::::::::::::: :: :::::::::::::::::::: d1ofda2 622 ----SPLSSIKHA---G-SPWELGVTEVHRVLMENQLRDRVLLRADGGLKTGWDVVMAAL 673 d1d3ga_ 312 AGASLVQLYTALTFWG----------------------------------P-PVVGKVKR 336 :::::::::::::::: : :::::::: d1ofda2 674 MGAEEYGFGSIAMIAEGCIMARVCHTNNCPVGVATQQERLRQRFKGVPGQVVNFFYFIAE 733 d1d3ga_ 337 ELEALLKEQGFGGVTDAIGAD------------------------H-R-R---------- 360 ::::::::::::::::::::: : : : d1ofda2 734 EVRSLLAHLGYRSLDDIIGRTDLLKVRSDVQLSKTQNLTLDCLLNLPDTKQNRQWLNHEP 793 HHsearch alignment (Probability: 0.99 E-value:0.00) d1d3ga_ 159 AAEDYAEGVRVLGPLADYLVVNVSSPNTAGLGKAELRRLLTKVLQERDGLRRVH-RPAVL 217 ::::::::::::::::::: :::: ::::::::::::::: :::::: ::::: d1ofda2 537 KVSEYIAMLRRSKPGVTLI-----SPPP--HHDIYSIEDLAQLIY---DLHQINPEAQVS 586 d1d3ga_ 218 VKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLS-------- 269 ::::: :::::::::::::::::::::::: ::::: d1ofda2 587 VKLVA---EIGIGTIAAGVAKANADIIQISGH---------------DGGTGASPLSSIK 628 d1d3ga_ 270 --GKPLRDLSTQTIREMYA--LTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTF 325 :::: :::::::::::: ::::::::::::::::::::::::::::::::::::::: d1ofda2 629 HAGSPW-ELGVTEVHRVLMENQLRDRVLLRADGGLKTGWDVVMAALMGAEEYGFGSIAMI 687 d1d3ga_ 326 ---------------------WGPP--------------VVGKVKRELEALLKEQGFGGV 350 :::: ::::::::::::::::::::: d1ofda2 688 AEGCIMARVCHTNNCPVGVATQQERLRQRFKGVPGQVVNFFYFIAEEVRSLLAHLGYRSL 747 d1d3ga_ 351 TDAIGAD 357 ::::::: d1ofda2 748 DDIIGRT 754