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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d2tpsa_ | Thiamin phosphate synthase | Thiamin phosphate synthase | TIM beta/alpha-barrel | α/β |
| Hit | d1d8ca_ | Malate synthase G | Malate synthase G | TIM beta/alpha-barrel | α/β |
Query <-- 0.821 --> IntermediateDALI alignment (Z-score: 9.1 Raw score:858.90) query 1 ---------------mietpyylidkakltRNMERIAHVREKSGAKALLALKC------f 39 ::::::::::::::::::::::: d2tpsa_ 1 hgirmtrisremmkellsvyfimgsnntkaDPVTVVQKALKGGATLYQFREKGgdaltge 60 query 40 aTWSVFDLMRDYM-----DGTTSSslfEVRLGRERfGKETHAYSVAYGdnEIDEVVSHA- 93 :::::::::::: :::::: :::::::: :::::::::::: ::::::::: d2tpsa_ 61 aRIKFAEKAQAACreagvPFIVND---DVELALNL-KADGIHIGQEDA--NAKEVRAAIg 114 query 94 --DKIIFNSI-SQLERFADKAagIARGLRLNPQ-------RLGEWDVPKVERVM---DRI 140 :::::::: :::::::::: :::::::::: :::::::::::::: ::: d2tpsa_ 115 dmILGVSAHTmSEVKQAEEDG--ADYVGLGPIYptetkkdTRAVQGVSLIEAVRrqgISI 172 query 141 NGFMIHNncenkdfglfdrMLGEIEeRFGALiaRVDWVSLggGIHFTGddYPVDAFSARL 200 ::::::: :::::: ::::: ::::::: :::::: :::::::::: d2tpsa_ 173 PIVGIGG-----------iTIDNAA-PVIQA--GADGVSM--ISAISQ-aEDPESAARKF 215 query 201 RAFSDRYGvqiylepgeasitksttlevtvldtlynknlaivdssieahmldlliyreta 260 :::::::: d2tpsa_ 216 REEIQTYK---------------------------------------------------- 223 query 261 kvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkm 320 d2tpsa_ 224 ------------------------------------------------------------ 224 query 321 paiaireldgsvrtvreftyadyeqsls 348 d2tpsa_ 224 -------------------------tgr 226 FAST alignment (Normalized score: 3.17 Raw score:888.50) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYM-------- 52 d2tpsa_ 1 ----------------------------------------------------HGIRMTRI 8 query 53 ----------DGTTSS--------SLFEVRLGRERF-GKETHAYSVAY-----------G 82 ::::: ::::::::::: ::::::: : d2tpsa_ 9 SREMMKELLSVYFIM-GSNNTKADPVTVVQKALKG-GATLYQFR----EKGGDALTGEAR 62 query 83 DNEIDEVVSHA-----DKIIFN-SISQLERFADKAAGIA---RGLRLNPQRLGE--WDVP 131 :::::::::: :::::: ::::::: ::::::: :::: d2tpsa_ 63 IKFAEKAQAA-CREAGVPFIVNDDVELALN---------LKADGIHIGQ-----EDANAK 107 query 132 KVERVMDRI--NGFMIHNNCENKDFGL--FDRMLGEIEERFGALIA-RVDWVSLGGGIHF 186 :::::: :::::: :::::::::: ::::::: d2tpsa_ 108 EVRAAI---GDMILGVS----------AHTMSEVKQAEE-------DGADYVGL------ 141 query 187 TGDDYPVDA----------------FSARLRAFSD-RYGVQIYLEPGEASITKSTTLEVT 229 :::::::::: ::::::::: :::: d2tpsa_ 142 ---------GPIYPTETKKDTRAVQGVSLIEAVRRQGISIPIVGI-GGIT---------- 181 query 230 VLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRF 289 d2tpsa_ 182 ------------------------------------------------------------ 182 query 290 AEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS- 348 d2tpsa_ 182 -----------------------------------------------------------I 182 query 349 -------------------------------------------- 349 d2tpsa_ 183 DNAAPVIQAGADGVSMISAISQAEDPESAARKFREEIQTYKTGR 226 TMalign alignment (TM-score: 0.41 Raw score:143.89) query 1 ----------------------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKA 32 ::::::::::::::::::: d2tpsa_ 1 HGIRMTRISREMMKELLSVYFIMGSNNT-------------KADPVTVVQKALKGGATLY 47 query 33 LLALKC--F-A---TWSVFDLMRDYM-----DGTTSSSLFEVRLGRERFGKETHAYSVAY 81 :::::: : : :::::::::::: :::::: : :::::::::::::::::: d2tpsa_ 48 QFREKGGDALTGEARIKFAEKAQAACREAGVPFIVND---D-VELALNLKADGIHIGQED 103 query 82 GDNEIDEVVS-H--ADKIIFN-SISQLERFADKAAGIARGLRLNPQ--------RLGE-W 128 : ::::::: : ::::::: :::::::::::: :::::::::: :::: : d2tpsa_ 104 A--NAKEVRAAIGDMILGVSAHTMSEVKQAEEDG--ADYVGLGPIYPTETKKDTRAVQGV 159 query 129 D-VPKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFT 187 : ::::::::::::::::::: ::: : ::::::::: : :::::::::: d2tpsa_ 160 SLIEAVRRQGISIPIVGIGGI--------TID--N-AAPVIQAGA--D--GVSMISAISQ 204 query 188 GDDYPVDAFSARLRAFSDRYGV--QIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSS 245 : ::::::::::::::::::: d2tpsa_ 205 A--EDPESAARKFREEIQTYKTGR------------------------------------ 226 query 246 IEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAA 305 d2tpsa_ 227 ------------------------------------------------------------ 227 query 306 GYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d2tpsa_ 227 ------------------------------------------- 227 HHsearch alignment (Probability: 0.39 E-value:0.03) query 9 IDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRE 68 :::::::::::::::::::::::::: :::::::::::::::::::::::::: :: d2tpsa_ 57 LTGEARIKFAEKAQAACREAGVPFIV----NDDVELALNLKADGIHIGQEDANAKE--VR 110 query 69 RFGKETHAYSVAYGDNEIDEVVSHADKII----------------FNSISQLERFADKAA 112 ::::::::::::::::::::::::::::: ::::::::::::::: d2tpsa_ 111 AAIGDMILGVSAHTMSEVKQAEEDGADYVGLGPIYPTETKKDTRAVQGVSLIEAVRRQGI 170 query 113 GIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGAL 171 :::::: ::::::::::::::::::::: ::::::::::::::::::::::::: d2tpsa_ 171 SIPIVG-----IGGITIDNAAPVIQAGADGVS--MISAISQAEDPESAARKFREEIQTY 222
Intermediate <-- 0.921 --> HitDALI alignment (Z-score: 9.8 Raw score:1254.40) d2tpsa_ 1 ------------------------------------------------------------ 1 d1d8ca_ 1 qtitqsrlridanfkrfvdeevlpgtgldaaafwrnfdeivhdlapenrqllaerdriqa 60 d2tpsa_ 1 -----------------------------------hgirmTRISrEMMKELLSVYFIMGS 25 :::: ::::::::::::::: d1d8ca_ 61 aldewhrsnpgpvkdkaayksflrelgylvpqpervtvetTGID-SEITSQAGPQLVVPA 119 d2tpsa_ 26 nntkaDPVTVVQKALKG------------------------------------------- 42 :::::::::::: d1d8ca_ 120 --mnaRYALNAANARWGslydalygsdiipqegamvsgydpqrgeqviawvrrfldeslp 177 d2tpsa_ 43 ------------------------------------------------------------ 43 d1d8ca_ 178 lengsyqdvvafkvvdkqlriqlkngkettlrtpaqfvgyrgdaaaptcillknnglhie 237 d2tpsa_ 43 -----------------------gATLYQFRE---KGGD-alTGEARIKFAEKAQAA--- 72 :::::::: :::: ::::::::::::::: d1d8ca_ 238 lqidangrigkddpahindviveaAISTILDCedsVAAVdaeDKILLYRNLLGLMQGtlq 297 d2tpsa_ 73 -----------------crEAGVPFIVND-----------------------DVELALNL 92 :::::::::: :::::::: d1d8ca_ 298 rklnddrhytaadgseislHGRSLLFIRNvghlmtipviwdsegneipegilDGVMTGAI 357 d2tpsa_ 93 K-------------aDGIHIGQE--daNAKEVRAAI-----------GDMILGVSAH--- 123 : :::::::: ::::::::: :::::::::: d1d8ca_ 358 AlydlkvqknsrtgsVYIVKPKMhgpqEVAFANKLFtrietmlgmapNTLKMGIMDEerr 417 d2tpsa_ 124 -TMSEvKQAEEDG---ADYVGLGPiyptetkkDTRA------------------------ 155 :::: ::::::: :::::::: :::: d1d8ca_ 418 tSLNL-RSCIAQArnrVAFINTGF--------LDRTgdemhsvmeagpmlrknqmkstpw 468 d2tpsa_ 156 -VQGVSLIEAVRRqGISI----PIVGIGG-------iTIDNAAPVIQAGADGVSMisAIS 203 :::::::::::: :::: ::::::: :::::::::::::::::: ::: d1d8ca_ 469 iKAYERNNVLSGL-FCGLrgkaQIGKGMWampdlmadMYSQKGDQLRAGANTAWV--PSP 525 d2tpsa_ 204 QaedpesAARKFREEIQTY-KTGR------------------------------------ 226 : :::::::::::: :::: d1d8ca_ 526 T------AATLHALHYHQTnVQSVqaniaqtefnaefepllddlltipvaenanwsaqei 579 d2tpsa_ 227 ------------------------------------------------------------ 227 d1d8ca_ 580 qqeldnnvqgilgyvvrwveqgigcskvpdihnvalmedratlrissqhianwlrhgilt 639 d2tpsa_ 227 ------------------------------------------------------------ 227 d1d8ca_ 640 keqvqaslenmakvvdqqnagdpayrpmagnfanscafkaasdliflgvkqpngytepll 699 d2tpsa_ 227 ---------- 227 d1d8ca_ 700 hawrlrekes 709 FAST alignment (Normalized score: 4.61 Raw score:1844.00) d2tpsa_ 1 HGIRMTRISREMMKE--------------------------------------------- 15 d1d8ca_ 1 ---------------QTITQSRLRIDANFKRFVDEEVLPGTGLDAAAFWRNFDEIVHDLA 45 d2tpsa_ 16 ------------------------------------------------------------ 16 d1d8ca_ 46 PENRQLLAERDRIQAALDEWHRSNPGPVKDKAAYKSFLRELGYLVPQPERVTVETTGIDS 105 d2tpsa_ 16 ----LLSVYFIMGSNNTKAD----PVTVVQKALKG------------------------- 42 ::::::: :::::::::: d1d8ca_ 106 EITSQAGPQLV---------VPAMNARYALNAAN-ARWGSLYDALYGSDIIPQEGAMVSG 155 d2tpsa_ 43 ------------------------------------------------------------ 43 d1d8ca_ 156 YDPQRGEQVIAWVRRFLDESLPLENGSYQDVVAFKVVDKQLRIQLKNGKETTLRTPAQFV 215 d2tpsa_ 43 ---------------------------------------------GATLYQFREKGGD-- 55 ::::::::::: d1d8ca_ 216 GYRGDAAAPTCILLKNNGLHIELQIDANGRIGKDDPAHINDVIVEAAISTILDCED--SV 273 d2tpsa_ 56 ALTGEARIKFAEKAQAACREA--------------------------GVPFIVND----- 84 ::::::::::::::::::: :::::: d1d8ca_ 274 AAVDAEDKILLYRNLLGLM--QGTLQRKLNDDRHYTAADGSEISLHGRSLLFI--RNVGH 329 d2tpsa_ 85 --------------------DVELALNLKA----------------DGIHIGQEDA---- 104 ::::::: ::::: d1d8ca_ 330 LMTIPVIWDSEGNEIPEGILDGVMTGA---IALYDLKVQKNSRTGSVYIVK-----PKMH 381 d2tpsa_ 105 ---NAKEVRAAI------------GDMILGVSAHTMS---EVKQAEE---DGADYVGLGP 143 :::::::: ::::::::::::: ::::::: :::::::: d1d8ca_ 382 GPQEVAFANKL-FTRIETMLGMAPNTLKMGIMDEERRTSLNLRSCIAQARNRVAFINT-- 438 d2tpsa_ 144 IYPTETKKDTRAV---------------------------------QGVSLIEAVRRQGI 170 ::::::::::::: d1d8ca_ 439 -------------GFLDRTGDEMHSVMEAGPMLRKNQMKSTPWIKAYERNNVLSGLFCG- 484 d2tpsa_ 171 ---SIPIVGIGGI----------TIDNAAPVIQAGADGVSMISAISQAED-PESAARKFR 216 ::::::: :::::::::::::::::: ::::::::: d1d8ca_ 485 LRGKAQIGKG---MWAMPDLMADMYSQKGDQLRAGANTAWV---------PSPTAATLHA 532 d2tpsa_ 217 EEIQT--YKTGR------------------------------------------------ 226 ::::: :::: d1d8ca_ 533 LHYHQTNVQSV-QANIAQTEFNAEFEPLLDDLLTIPVAENANWSAQEIQQELDNNVQGIL 591 d2tpsa_ 227 ------------------------------------------------------------ 227 d1d8ca_ 592 GYVVRWVEQGIGCSKVPDIHNVALMEDRATLRISSQHIANWLRHGILTKEQVQASLENMA 651 d2tpsa_ 227 ---------------------------------------------------------- 227 d1d8ca_ 652 KVVDQQNAGDPAYRPMAGNFANSCAFKAASDLIFLGVKQPNGYTEPLLHAWRLREKES 709 TMalign alignment (TM-score: 0.71 Raw score:160.09) d2tpsa_ 1 ------------------------------------------------------------ 1 d1d8ca_ 1 QTITQSRLRIDANFKRFVDEEVLPGTGLDAAAFWRNFDEIVHDLAPENRQLLAERDRIQA 60 d2tpsa_ 1 ---------------------------------------HGIRMTRISREMMKELLSVYF 21 :::::::::::::::: d1d8ca_ 61 ALDEWHRSNPGPVKDKAAYKSFLRELGYLVPQPERVTVE-----TTGIDSEITSQAGPQL 115 d2tpsa_ 22 IMGSNNTKADPVTVVQKALKG--------------------------------------- 42 ::::: : ::::::::::::: d1d8ca_ 116 VVPAM-N-ARYALNAANARWGSLYDALYGSDIIPQEGAMVSGYDPQRGEQVIAWVRRFLD 173 d2tpsa_ 43 ------------------------------------------------------------ 43 d1d8ca_ 174 ESLPLENGSYQDVVAFKVVDKQLRIQLKNGKETTLRTPAQFVGYRGDAAAPTCILLKNNG 233 d2tpsa_ 43 ---------------------------GATLYQFREKG-GDA---LTGEARIKFAEKAQ- 70 ::::::::::: ::: :::::::::::::: d1d8ca_ 234 LHIELQIDANGRIGKDDPAHINDVIVEAAISTILDCEDSVAAVDAEDKILLYRNLLGLMQ 293 d2tpsa_ 71 A-----ACRE--------------AGVPFIVND-----------------------DVEL 88 : :::: ::::::::: :::: d1d8ca_ 294 GTLQRKLNDDRHYTAADGSEISLHGRSLLFIRNVGHLMTIPVIWDSEGNEIPEGILDGVM 353 d2tpsa_ 89 ALNLK--A-----------DGIHIG-QE---DA-NAKEVRA-AI-------GDMILGVSA 122 ::::: : :::::: :: :: ::::::: :: ::::::::: d1d8ca_ 354 TGAIALYDLKVQKNSRTGSVYIVKPKMHGPQEVAFANKLFTRIETMLGMAPNTLKMGIMD 413 d2tpsa_ 123 H----TMSEVKQAEEDG--ADYVGLGPIYPTETKKDTRA------------------VQ- 157 : :::::::::::: :::::::: : ::: :: d1d8ca_ 414 EERRTSLNLRSCIAQARNRVAFINTGF---L-----DRTGDEMHSVMEAGPMLRKNQMKS 465 d2tpsa_ 158 ---GVSLIEAVRRQ-GI-SI----PIVGIGGI-------TIDNAAPVIQAGADGVSMISA 201 ::::::::::: :: :: :::::::: :::::::::::::::::: : d1d8ca_ 466 TPWIKAYERNNVLSGLFCGLRGKAQIGKGMWAMPDLMADMYSQKGDQLRAGANTAWV--P 523 d2tpsa_ 202 ISQAEDPESAARKFREEIQTYKT-GR---------------------------------- 226 : : ::::::::::::::: :: d1d8ca_ 524 S-----P-TAATLHALHYHQTNVQSVQANIAQTEFNAEFEPLLDDLLTIPVAENANWSAQ 577 d2tpsa_ 227 ------------------------------------------------------------ 227 d1d8ca_ 578 EIQQELDNNVQGILGYVVRWVEQGIGCSKVPDIHNVALMEDRATLRISSQHIANWLRHGI 637 d2tpsa_ 227 ------------------------------------------------------------ 227 d1d8ca_ 638 LTKEQVQASLENMAKVVDQQNAGDPAYRPMAGNFANSCAFKAASDLIFLGVKQPNGYTEP 697 d2tpsa_ 227 ------------ 227 d1d8ca_ 698 LLHAWRLREKES 709 HHsearch alignment (Probability: 0.01 E-value:0.33) d2tpsa_ 17 LSVYFIMGSNNTK------ADPVTVVQKALKGGATLYQFREKGGDALTGEARIKFAEKAQ 70 ::::::::::::: ::::::::::::::::::::::::::::::::::::::::: d1d8ca_ 371 GSVYIVKPKMHGPQEVAFANKLFTRIETMLGMAPNTLKMGIMDEERRTSLNLRSCIAQAR 430 d2tpsa_ 71 AACREAGVPFIVNDDVELA 89 : ::::::::::::: d1d8ca_ 431 N-----RVAFINTGFLDRT 444