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 <-- 1.488 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1qw9a2) 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 d1qw9a2 Alpha-​L-​arabinofuranosidase,​ catalytic domain(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 <-- 1.488 --> Hit
DALI alignment (Z-score: 11.1 Raw score:1271.80) d1thfd_ 1 MLAKR-IIACLDvkdgrVVKGsnfenlrDSGD-----------pvelgKFYSEI-GIDEL 47 ::::: :::::: :::: :::: :::::: ::::: d1qw9a2 1 EIDKRiYGSFIE-----HLGR----avyGGIYepghpqadengfrqdvIELVKElQVPII 51 d1thfd_ 48 VF-LDIT-ASVEKRKT--------------------mleLVEKVAEQID---IPFTVGGG 82 :: :::: :::::::: :::::::::: :::::::: d1qw9a2 52 RYpGGNFvSGYNWEDGvgpkeqrprrldlawksvetneiGLNEFMDWAKmvgAEVNMAVN 111 d1thfd_ 83 I--HDFETASELILRG----------------------ADKVSIN----------taaVE 108 : ::::::::::::: ::::::: :: d1qw9a2 112 LgtRGIDAARNLVEYCnhpsgsyysdlriahgykephkIKTWCLGnamdgpwqighktAV 171 d1thfd_ 109 NP-SLITQIAQTFG----sQAVVVAI-DAKRvdgefmvftysgkkntgILLRDWVVEVEK 162 :: ::::::::::: ::::::: :::: :::::::::::: d1qw9a2 172 EYgRIACEAAKVMKwvdptIELVVCGsSNRN----------------mPTFAEWEATVLD 215 d1thfd_ 163 RG---AGEILLTsidRDGT-----------ksgyDTEMIRFVRPLT-----------TLP 197 :: ::::::: :::: :::::::::::: ::: d1qw9a2 216 HTydhVDYISLH---QYYGnrdndtanylalsleMDDFIRSVVAIAdyvkakkrskkTIH 272 d1thfd_ 198 IIA-SGGA-------------------------------GKMEHFLEAFLA--GADAALA 223 ::: :::: :::::::::::: ::::::: d1qw9a2 273 LSFdEWNVwyhsneadkliepwtvappllediynfedalLVGCMLITLMKHadRVKIACL 332 d1thfd_ 224 A-----SVFHF---------REID--VRELKEYLKkhgvnvrlegl 253 : ::::: :::: ::::::::: d1qw9a2 333 AqlvnvIAPIMtekngpawkQTIYypFMHASVYGR----------- 367 FAST alignment (Normalized score: 5.48 Raw score:1670.00) d1thfd_ 1 MLAK-----RIIACLDVKDGRVVKGSNFENLRDSGD------------------------ 31 :::::: d1qw9a2 1 ----EIDKRIYGSFI---------------------EHLGRAVYGGIYEPGHPQADENGF 35 d1thfd_ 32 PVELGKFYSEIGIDELVFL---DITASVEKRK---------------------------- 60 ::::::::::::::::: ::::: d1qw9a2 36 RQDVIELVKELQVPIIR--YPGGNFVS-----GYNWEDGVGPKEQRPRRLDLAWKSVETN 88 d1thfd_ 61 --TMLELVEKVAEQIDIPFTVGGGI-----HDFETASELIL------------------- 94 :::::::: ::::::::::: ::::::::::: d1qw9a2 89 EIGLNEFMDW-AKMVGAEVNMA---VNLGTRGIDAARNLVEYCNHPSGSYYSDLRIAHGY 144 d1thfd_ 95 ---RGADKVSINTAAVEN-----------------------PSLITQIAQTFGSQ-AVVV 127 ::::::: :::::::::: ::: :::: d1qw9a2 145 KEPHKIKTWC--------LGNAMDGPWQIGHKTAVEYGRIACEAAKVMKWV-DPTIELVV 195 d1thfd_ 128 AIDAKRVDGEFMVFTYSGKKNTGI--------LLRDWVVEVEK---RGAGEILLTSIDRD 176 : ::::::::::: :::::::::: d1qw9a2 196 C-----------------------GSSNRNMPTFAEWEATVLDHTYDHVDYISLHQ---- 228 d1thfd_ 177 GTKSGY------------------DTEMIRFVRPLT------------TLPIIASGGAG- 205 ::::::::::: ::::::::: d1qw9a2 229 ------YYGNRDNDTANYLALSLEMDDFIRSVVAI-ADYVKAKKRSKKTIHLSFDEW--N 279 d1thfd_ 206 ---------------------------------KMEHFLEAFL--AGADAALAASVFHFR 230 :::::::::: ::::::: d1qw9a2 280 VWYHSNEADKLIEPWTVAPPLLEDIYNFEDALLVGCMLITLMKHADRVKIAC-------- 331 d1thfd_ 231 EI--------------------------DVRELKEYLKKHGVNVRLEGL- 253 ::::::::: d1qw9a2 332 --LAQLVNVIAPIMTEKNGPAWKQTIYYPFMHASVYG------------R 367 TMalign alignment (TM-score: 0.67 Raw score:168.96) d1thfd_ 1 MLAK-RIIACLDVKDGRVVKGS-NF---ENLRDS--GDPVELGKFYSEIGIDELVFLD-I 52 :::: ::::::::::::::::: : :::: :::::::::::::::::::::: : d1qw9a2 1 EIDKRIYGSFIEHLGRAVYGGIY-EPGH--PQADENGFRQDVIELVKELQVPIIRYPGGN 57 d1thfd_ 53 TA-SVEKRKT-----------------------MLELVEKVAEQIDIPFTVGGGI--H-- 84 :: ::::::: :::::::::::::::::::::: : d1qw9a2 58 FVSGYNWEDGVGPKEQRPRRLDLAWKSVETNEIGLNEFMDWAKMVGAEVNMAVNLGTRGI 117 d1thfd_ 85 --DFETASELIL-----------------RG-ADKVSIN--T------------AAVEN- 109 :::::::::: :: ::::::: : ::::: d1qw9a2 118 DAARNLVEYCNHPSGSYYSDLRIAHGYKEPHKIKTWCLGNAMDGPWQIGHKTAVEYGRIA 177 d1thfd_ 110 PSLITQIAQTFGSQAVVVAIDA-KRVDGEFMVFTYSGKKNTGILLRDWVVEVEKRGAGEI 168 :::::::::::::::::::::: :::: ::: ::::::::::::: :::: d1qw9a2 178 CEAAKVMKWVDPTIELVVCGSSNRNMP-TFA-----------EWEATVLDHTYDH-VDYI 224 d1thfd_ 169 LLTSIDRDGTK-------S--GY--DTEMIRFVRP-LT----------TLPIIASGGAG- 205 :::: : ::: : :: :::::::::: :: ::::::::::: d1qw9a2 225 SLHQ--Y-YGNRDNDTANYLALSLEMDDFIRSVVAIADYVKAKKRSKKTIHLSFDEWNVW 281 d1thfd_ 206 -------------------------------KMEHFLEAFLA--GADAALA-A----SVF 227 ::::::::::: ::::::: : ::: d1qw9a2 282 YHSNEADKLIEPWTVAPPLLEDIYNFEDALLVGCMLITLMKHADRVKIACLAQLVNVIAP 341 d1thfd_ 228 HF---------R-EID-VRELKEYLKKHGVNVRLEGL 253 :: : ::: :::::: : :: d1qw9a2 342 IMTEKNGPAWKQTIYYPFMHASV--Y-----GR---- 367 HHsearch alignment (Probability: 0.01 E-value:0.18) d1thfd_ 34 ELGKFYSEIGIDELVFLD 51 :::::::::::::::::: d1qw9a2 94 EFMDWAKMVGAEVNMAVN 111