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 <-- 1.415 --> Intermediate <-- 1.392 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1g5aa2) through the intermediate protein (d1thfd_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1thfd_ Cyclase subunit (or domain) of imidazoleglycerolphosphate synthase HisFRibulose-​phoshate binding barrelTIM beta/​alpha-​barrelα/β
Hit d1g5aa2 Amylosucrase(Trans)glycosidasesTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 1.415 --> Intermediate
DALI alignment (Z-score: 10.2 Raw score:987.30) query 1 mietpyylidkakltrnmeriahvreksGAKALLALK-----------------cfATWS 43 ::::::::: :::: d1thfd_ 1 --------------------------mlAKRIIACLDvkdgrvvkgsnfenlrdsgDPVE 34 query 44 VFDLMR-DYMDGTTSS-----------SLFEVRLGRERFGKETHAYSV-AYGDnEIDEVV 90 :::::: ::::::::: ::::::::::::::::::::: :::: :::::: d1thfd_ 35 LGKFYSeIGIDELVFLditasvekrktMLELVEKVAEQIDIPFTVGGGiHDFE-TASELI 93 query 91 S-HADKIIFNS-----ISQLERFADKAAgIARGLRLNPQ---------------rlgeWD 129 : ::::::::: :::::::::::: :::::::::: :: d1thfd_ 94 LrGADKVSINTaavenPSLITQIAQTFGsQAVVVAIDAKrvdgefmvftysgkkntgiLL 153 query 130 VPKVERVMD-RINGFMIHN--NCENKDFglfdrMLGEIEeRFGALIarVDWVSLGGGIHF 186 ::::::::: ::::::::: ::::::: :::::: :::::: :::::::::::: d1thfd_ 154 RDWVVEVEKrGAGEILLTSidRDGTKSG----yDTEMIR-FVRPLT--TLPIIASGGAGK 206 query 187 tgddypvDAFSARLRAFSdrygvqIYLEPGEASITksttlevtvldtlynknlaivdssi 246 ::::::::::: ::::::::::: d1thfd_ 207 -------MEHFLEAFLAG-----aDAALAASVFHF------------------------- 229 query 247 eahmldlliyretakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaag 306 d1thfd_ 230 ------------------------------------------------------------ 230 query 307 ytmvkknwfngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1thfd_ 230 ------------------reidvrelkeylkkhgvnvrlegl 253 FAST alignment (Normalized score: 5.37 Raw score:1594.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS--GAKALLALKCFA------------------ 40 ::::::: d1thfd_ 1 ----------------------------MLAKRIIAC-----LDVKDGRVVKGSNFENLR 27 query 41 ----TWSVFDLMRD-YMDGTTSS------------SLFEVRLGRERFGKETHAYSVAY-G 82 :::::::::: ::::::: :::::::::::::::::: :::: : d1thfd_ 28 DSGDPVELGKFYSEIGIDELVF-LDITASVEKRKTMLELVEKVAEQIDIPFTV-GGGIHD 85 query 83 DNEIDEVV-SHADKIIFNSISQLERFADK----AAGI---ARGLRLNPQRLGEW------ 128 :::::::: :::::::: :::::::::: :::: ::::::: d1thfd_ 86 FETASELILRGADKVSI--NTAAVENPSLITQIAQTFGSQAVVVAID-------AKRVDG 136 query 129 ----------------DVPKVERVMD-RINGFMIHN----NCENKDFGLFDRMLGE---I 164 :::::::::: ::::::: ::::: : d1thfd_ 137 EFMVFTYSGKKNTGILLRDWVVEVEKRGAGEILL--TSIDRDGTK-----------SGYD 183 query 165 EERFGALIARV-DWVSLGGGIHFTGDDYPVDA-FSARLRAFSDRYGVQIYLEPGEASITK 222 ::::::::::: ::::::::: :::::::::: ::: ::::::::: d1thfd_ 184 TEMIRFVRPLTTLPIIASGGA-----------GKMEHFLEAFL-AGA-DAALAASVF--- 227 query 223 STTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGD 282 d1thfd_ 228 ------------------------------------------------------------ 228 query 283 VFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYAD 342 d1thfd_ 228 ------------------------------------------------------------ 228 query 343 YEQSLS-------------------------- 348 d1thfd_ 228 ------HFREIDVRELKEYLKKHGVNVRLEGL 253 TMalign alignment (TM-score: 0.36 Raw score:125.07) query 1 -------------MIETPYYLID---------KAK-L-TRNMERIAHVREKSGAKALLAL 36 :::: ::: : :::::::::: :: : :::::: d1thfd_ 1 MLAKRIIACLDVK------DGRVVKGSNFENLRDSGDPVELGKFYSEI-GI-D-ELVFLD 51 query 37 --KC--FA-T-WSVFDLMR--D-YMDGTT--SSSLFEVRLGRERFGKETHAY-S-VAYGD 83 :: :: : :::::::: : :::::: ::::::::::::::::::::: : ::::: d1thfd_ 52 ITASVEKRKTMLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVSINTAAVENPS 111 query 84 NEIDEVVSHADKIIFNSISQLERFADKAAGIARGLRLNPQ------RL-------G-EWD 129 :::::::::::: :::::::::: :: : ::: d1thfd_ 112 -LITQIAQTFGSQ-----------------AVVVAIDAKRVDGEFMVFTYSGKKNTGILL 153 query 130 VPKVERVMDR-I-NGFMIHNNCENKDFGLFDRMLGEIEERFGALIA-RVDWVSLGGGIHF 186 : :::::::: : :::::::::::: :::: : :::::::::: ::::::::: : : d1thfd_ 154 R-DWVVEVEKRGAGEILLTSIDRDG---TKSG-Y--DTEMIRFVRPLTTLPIIASG-G-A 204 query 187 TGDDYPVDAFSARLRAFSDRYGVQIYLEP--GEAS------------------------- 219 : :: ::::::: :::::::::: :: d1thfd_ 205 -----G--KM-EHFLEAF-LAGADAALAASV--FHFREIDVRELKEYLKKHGVNVRLEGL 253 query 220 ITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCL 279 d1thfd_ 254 ------------------------------------------------------------ 254 query 280 AGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFT 339 d1thfd_ 254 ------------------------------------------------------------ 254 query 340 YADYEQSLS 348 d1thfd_ 254 --------- 254 HHsearch alignment (Probability: 0.08 E-value:0.02) query 62 EVRLGRERFGKETHAYSVAYGD-NEIDEVVSHADKIIF------NSISQLERFADKAAGI 114 :::::::::::::::::::::: ::::::::::::::: :::::::::::::::: d1thfd_ 185 EMIRFVRPLTTLPIIASGGAGKMEHFLEAFLAGADAALAASVFHFREIDVRELKEYLKKH 244 query 115 ARGLRLNP 122 :::::::: d1thfd_ 245 GVNVRLEG 252
Intermediate <-- 1.392 --> Hit
DALI alignment (Z-score: 11.4 Raw score:1154.90) d1thfd_ 1 ------------------------------------------------------------ 1 d1g5aa2 1 spnsqylktrildiytpeqragieksedwrqfsrrmdthfpklmneldsvygnneallpm 60 d1thfd_ 1 ---------------------------------mLAKRIIACLDvkdgRVVKgsnfenlr 27 :::::::::: :::: d1g5aa2 61 lemllaqawqsysqrnsslkdidiarennpdwilSNKQVGGVCY----VDLF-------- 108 d1thfd_ 28 dSGDP---VELGKFYSEIGIDELVFLD----------ITAS-VEKRKT-----mLELVEK 68 :::: ::::::::::::::::::: :::: :::::: :::::: d1g5aa2 109 -AGDLkglKDKIPYFQELGLTYLHLMPlfkcpegksdGGYAvSSYRDVnpalgtIGDLRE 167 d1thfd_ 69 VAEQID---IPFTVGggIH----------------------------------------- 84 :::::: :::::: :: d1g5aa2 168 VIAALHeagISAVVD--FIfnhtsnehewaqrcaagdplfdnfyyifpdrrmpdqydrtl 225 d1thfd_ 85 ------------------------------------------DFETASELILRGADKVSI 102 :::::::::::::::::: d1g5aa2 226 reifpdqhpggfsqledgrwvwttfnsfqwdlnysnpwvfraMAGEMLFLANLGVDILRM 285 d1thfd_ 103 NTaAV-----------EN---PSLITQIAQTFG----sQAVVVAIDAkrvdgefmvftys 144 :: :: :: :::::::::::: ::::::::: d1g5aa2 286 DA-VAfiwkqmgtsceNLpqaHALIRAFNAVMRiaapaVFFKSEAIV------------- 331 d1thfd_ 145 gkkntgiLLRDWVvEVEK-RGAGEILLTSidrdgtksgYD-------------TE-MIRF 189 :::::: :::: :::::::::: :: :: :::: d1g5aa2 332 -------HPDQVV-QYIGqDECQIGYNPL--------qMAllwntlatrevnlLHqALTY 375 d1thfd_ 190 VRPLTT-LPIIASG---------------------------------------------- 202 :::::: ::::::: d1g5aa2 376 RHNLPEhTAWVNYVrshddigwtfadedaaylgisgydhrqflnrffvnrfdgsfargvp 435 d1thfd_ 203 -----------------------------gagkmehFLEAFLaGADAALAAsvFHFRE-- 231 :::::: :::::::: ::::: d1g5aa2 436 fqynpstgdcrvsgtaaalvglaqddphavdrikllYSIALS-TGGLPLIY--LGDEVgt 492 d1thfd_ 232 -------------------------------------------iDVRELKEYL-KKHGVN 247 ::::::::: :::::: d1g5aa2 493 lndddwsqdsnksddsrwahrprynealyaqrndpstaagqiyqDLRHMIAVRqSNPRFD 552 d1thfd_ 248 vrlegl 253 d1g5aa2 553 ----gg 554 FAST alignment (Normalized score: 4.50 Raw score:1687.00) d1thfd_ 1 MLA--------------------------------------------------------- 3 d1g5aa2 1 ---SPNSQYLKTRILDIYTPEQRAGIEKSEDWRQFSRRMDTHFPKLMNELDSVYGNNEAL 57 d1thfd_ 4 ---------------------------------------KRIIACLDVKDGRVVKGSNFE 24 :::::::: d1g5aa2 58 LPMLEMLLAQAWQSYSQRNSSLKDIDIARENNPDWILSNKQVGGVCY------------- 104 d1thfd_ 25 NLRDSG---------DPVELGKFYSEIGIDELVFLDITASVE------------------ 57 ::::::::::::::::::: d1g5aa2 105 ------VDLFAGDLKGLKDKIPYFQELGLTYLHL--------MPLFKCPEGKSDGGYAVS 150 d1thfd_ 58 ----------KRKTMLELVEKVAEQIDIPFTVGGGIH----------------------- 84 ::::::::::::: :::::::: d1g5aa2 151 SYRDVNPALGTIGDLREVIAALH-EAGISAVV-----DFIFNHTSNEHEWAQRCAAGDPL 204 d1thfd_ 85 ------------------------------------------------------------ 85 d1g5aa2 205 FDNFYYIFPDRRMPDQYDRTLREIFPDQHPGGFSQLEDGRWVWTTFNSFQWDLNYSNPWV 264 d1thfd_ 85 ---DFETASELILRGADKVSINTAAVE------------------NPSLITQIAQTFGSQ 123 ::::::::::::::::::: ::::::::::: d1g5aa2 265 FRAMAGEMLFLANLGVDILRMD-----AVAFIWKQMGTSCENLPQAHALIRAFNAV---- 315 d1thfd_ 124 --------AVVVAIDAKRVDGEFMVFTYSGKKNTGIL-LRDWVVEVEKR----GAGEILL 170 ::::::: :::::::: ::::::: d1g5aa2 316 MRIAAPAVFFKSEAI----------------------VHPDQVVQY---IGQDECQIGYN 350 d1thfd_ 171 TSIDRDGTKSGY------------------DTEMIRFVRPL---TTLPIIASGGAG---- 205 ::::::::: ::::::: d1g5aa2 351 ------------PLQMALLWNTLATREVNLLHQALTYRH--NLPEHTAWVN-----YVRS 391 d1thfd_ 206 ------------------------------------------------------------ 206 d1g5aa2 392 HDDIGWTFADEDAAYLGISGYDHRQFLNRFFVNRFDGSFARGVPFQYNPSTGDCRVSGTA 451 d1thfd_ 206 ----------------KMEHFLEAFLAGADAALAASVFHFREID---------------- 233 :::::::::::: :::: d1g5aa2 452 AALVGLAQDDPHAVDRIKLLYSIALSTG-GLPL-----------IYLGDEVGTLNDDDWS 499 d1thfd_ 234 -------------------------------VRELKEYLKKHGVNVRLEGL--------- 253 :::::::::: d1g5aa2 500 QDSNKSDDSRWAHRPRYNEALYAQRNDPSTAAGQIYQDLRH----------MIAVRQSNP 549 d1thfd_ 254 ----- 254 d1g5aa2 550 RFDGG 554 TMalign alignment (TM-score: 0.65 Raw score:164.93) d1thfd_ 1 ------------------------------------------------------------ 1 d1g5aa2 1 SPNSQYLKTRILDIYTPEQRAGIEKSEDWRQFSRRMDTHFPKLMNELDSVYGNNEALLPM 60 d1thfd_ 1 ---------------------------------MLAKRIIACLDVKDGRVVKGSNFENLR 27 ::::::::::: :::: d1g5aa2 61 LEMLLAQAWQSYSQRNSSLKDIDIARENNPDWILSNKQVGGVCY----VDLF-------- 108 d1thfd_ 28 DSG--DPVELGKFYSEIGIDELVFLD----------ITASVEKR-KTM----LE-LVEKV 69 ::: ::::::::::::::::::::: :::::::: ::: :: ::::: d1g5aa2 109 AGDLKGLKDKIPYFQELGLTYLHLMPLFKCPEGKSDGGYAVSSYRDVNPALGTIGDLREV 168 d1thfd_ 70 AEQI--D-IPFTVGGGIH------------------------------------------ 84 :::: : :::::::::: d1g5aa2 169 IAALHEAGISAVVDFIFNHTSNEHEWAQRCAAGDPLFDNFYYIFPDRRMPDQYDRTLREI 228 d1thfd_ 85 ---------------------------------------DFETASELILRGADKVSINTA 105 ::::::::::::::::::::: d1g5aa2 229 FPDQHPGGFSQLEDGRWVWTTFNSFQWDLNYSNPWVFRAMAGEMLFLANLGVDILRMDAV 288 d1thfd_ 106 AVE----------------NP-SLITQIAQTFGSQAVVVAIDAKRVDGEFMVFTYSGKKN 148 ::: :: ::::::::::: :::::::::: : d1g5aa2 289 AFIWKQMGTSCENLPQAHALIRAFNAVMRIAAP-AVFFKSEAIV------H--------- 332 d1thfd_ 149 TGILLRDWVVEVEKRGAGEILLTSIDRD-GTKSG------YDTEMIR-FVRPLTT-LPII 199 :::::::::::::::::::::::: :::: :::::: ::::::: :::: d1g5aa2 333 ----PDQVVQYIGQDECQIGYNPLQMALL-WNTLATREVN-LLHQALTYRHNLPEHTAWV 386 d1thfd_ 200 ASGG-------------------------------------------------------- 203 :::: d1g5aa2 387 NYVRSHDDIGWTFADEDAAYLGISGYDHRQFLNRFFVNRFDGSFARGVPFQYNPSTGDCR 446 d1thfd_ 204 ----AG---------------KMEHFLEAFLAGADAALAA-SVFH-F------------- 229 :: :::::::::: :::::::: :::: : d1g5aa2 447 VSGTAAALVGLAQDDPHAVDRIKLLYSIALS-TGGLPLIYLGDEVGTLNDDDWSQDSNKS 505 d1thfd_ 230 ---------------R---------E--IDVRELKEYLKKHGVNVRL------EGL 253 : : :: :::::::: ::::: d1g5aa2 506 DDSRWAHRPRYNEALYAQRNDPSTAAGQIY-QDLRHMIA---VRQSNPRFDGG--- 554 HHsearch alignment (Probability: 0.00 E-value:0.35) d1thfd_ 192 PLTTLPIIASGGA 204 ::::::::::::: d1g5aa2 477 STGGLPLIYLGDE 489