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 <-- 1.541 --> Intermediate <-- 1.304 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1iexa1) through the intermediate protein (d1q6oa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1q6oa_ 3-​keto-​L-​gulonate 6-​phosphate decarboxylaseRibulose-​phoshate binding barrelTIM beta/​alpha-​barrelα/β
Hit d1iexa1 Beta-​D-​glucan exohydrolase,​ N-​terminal domain(Trans)glycosidasesTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 1.541 --> Intermediate
DALI alignment (Z-score: 13.1 Raw score:1148.30) query 1 mietpyylidkakltrnmeriahvreksGAKALLALKC---fATWSVFDLMRDYMDGTTS 57 :::::::::: :::::::::::::::::: d1q6oa_ 1 ----------------------------LPMLQVALDNqtmdSAYETTRLIAEEVDIIEV 32 query 58 S-------SLFEVRLGRERFG-KETHAYS-VAYG-DNEIDEVVS-HADKIIFNS---ISQ 103 : ::::::::::::: ::::::: :::: ::::::::: ::::::::: ::: d1q6oa_ 33 GtilcvgeGVRAVRDLKALYPhKIVLADAkIADAgKILSRMCFEaNADWVTVICcadINT 92 query 104 LERFADKAA--GIARGLRLNPQrlgeWDVPKVERVM-DRINGFMIHNNCE-NKDFgLFDR 159 ::::::::: ::::::::::: :::::::::: ::::::::::::: :::: :::: d1q6oa_ 93 AKGALDVAKefNGDVQIELTGY----WTWEQAQQWRdAGIGQVVYHRSRDaQAAG-VAWG 147 query 160 mlGEIEERFGALIARVDWVSLGGGIHFtgddypvdAFSARLRAFSdrygvQIYLEPGEAS 219 ::::::::::::::::::::::::: :::::::::: :::::::::: d1q6oa_ 148 --EADITAIKRLSDMGFKVTVTGGLAL--------EDLPLFKGIP-----IHVFIAGRSI 192 query 220 -ITKSttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsymicgksc 278 :::: d1q6oa_ 193 rDAAS------------------------------------------------------- 197 query 279 lagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvref 338 d1q6oa_ 198 ------------------------------------------------------pveaar 203 query 339 tyadyeqsls 348 d1q6oa_ 204 qfkrsiaelw 213 FAST alignment (Normalized score: 5.19 Raw score:1413.00) query 1 MIETPYYL----------IDKAKLTRNMERIAHVREKSGAKALLALKCFA----TWSVFD 46 ::::::::::: :::::: ::::: :::: :::::: d1q6oa_ 1 --------LPMLQVALDNQTMDSAYETTR---LIAEEV-DIIEV-GTIL-CVGEGVRAVR 46 query 47 LMRDYM-----DGTTSS-----SLFEVRLGRERF--GKETHAYSVAYGDNEIDEVVSHA- 93 ::::: ::::: :::::::::: ::::: :::::::::::::::: d1q6oa_ 47 DLKAL-YPHKIVLADA-KIADAGKILSRMCFE--ANADWVT-VICCADINTAKGALDV-A 100 query 94 ----DKIIF-----NSISQLERFADKAAGIARGLRLNPQRLGEW---------------D 129 ::::: ::::::::::: ::: :::::: : d1q6oa_ 101 KEFNGDVQIELTGYWTWEQAQQWRD--AGI-GQVVYH-------RSRDAQAAGVAWGEAD 150 query 130 VPKVERVMDRI--NGFMIHNNCENKDFGL---FDRMLGEIEERFGALIARVDWVSLGGGI 184 ::::::::: :::::: ::::: ::::: ::::::: d1q6oa_ 151 ITAIKRLSD--MGFKVTVT----------GGLALEDL----PLFKG--IPIHVFI----- 187 query 185 HFTGDD--------YPVDAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYN 236 ::::::::::::::::: d1q6oa_ 188 ------AGRSIRDAASPVEAARQFKRSIAEL----------------------------- 212 query 237 KNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVG 296 d1q6oa_ 213 ------------------------------------------------------------ 213 query 297 DRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS- 348 d1q6oa_ 213 ----------------------------------------------------W 213 TMalign alignment (TM-score: 0.43 Raw score:149.47) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF---ATWSVFDLMRDYMDGTTS 57 ::::::::::: :::::::::::::::::: d1q6oa_ 1 ----------------------------LPMLQVALDNQTMDSAYETTRLIAEEVDIIEV 32 query 58 -S--S----LFEVRLGRERFG-KETHAYSVAY-G-DNEIDEVVS-HADKIIFN--S-ISQ 103 : : :::::::::::: :::::::::: : ::::::::: :::::::: : ::: d1q6oa_ 33 GTILCVGEGVRAVRDLKALYPHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINT 92 query 104 LERFADKAA--GIARGLRLNPQRLGEWDVPKVERVMD-RINGFMIHNNCE-NK--DFGLF 157 ::::::::: ::::::::: : :::::::::::: :::::::::::: :: ::: d1q6oa_ 93 AKGALDVAKEFNGDVQIELT---G-YWTWEQAQQWRDAGIGQVVYHRSRDAQAAG--VAW 146 query 158 DRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGE 217 : ::::::::::::::::::::::::: : ::::::::: :: :::::: d1q6oa_ 147 -G--EADITAIKRLSDMGFKVTVTGGLAL-----E---DLPLFKGIP----IH-VFIAGR 190 query 218 ASITKST----------------TLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAK 261 ::::::: d1q6oa_ 191 SIRDAASPVEAARQFKRSIAELW------------------------------------- 213 query 262 VLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMP 321 d1q6oa_ 214 ------------------------------------------------------------ 214 query 322 AIAIRELDGSVRTVREFTYADYEQSLS 348 d1q6oa_ 214 --------------------------- 214 HHsearch alignment (Probability: 0.38 E-value:0.02) query 16 RNMERIAHVREKSGAKALLALKCFATWSV-FDLMRDYMDGTTSSS--------LFEVRLG 66 :::::::::: ::::::::::::::::: ::::::::::::::: ::::::: d1q6oa_ 43 RAVRDLKALY--PHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINTAKGALDVA 100 query 67 RERFGKETHAYSVAYGDNEIDEVVSHADKIIF-------------NSISQLERFADKAAG 113 :::::::::::::::::::::::::::::::: :::::::::::: :: d1q6oa_ 101 KEFNGDVQIELTGYWTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRL-SD 159 query 114 IARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGAL 171 :::::::::::::::::::::::::::: ::::::::::::::::::::::::: d1q6oa_ 160 MGFKVTVTGGLALEDLPLFKGIPIHVFI-----AGRSIRDAASPVEAARQFKRSIAEL 212
Intermediate <-- 1.304 --> Hit
DALI alignment (Z-score: 10.7 Raw score:1217.80) d1q6oa_ 1 -----------------------------lpMLQVALdnqtmdsayeTTRLIAE--EVDI 29 :::::: ::::::: :::: d1iexa1 1 dyvlykdatkpvedrvadllgrmtlaekigqMTQIER--------lvATPDVLRdnFIGS 52 d1q6oa_ 30 IEVGTILC--vgegvravRDLKALYP----------HKIVLADAK--------------- 62 :::::::: :::::::: ::::::::: d1iexa1 53 LLSGGGSVprkgatakewQDMVDGFQkacmstrlgiPMIYGIDAVhgqnnvygatifphn 112 d1q6oa_ 63 -----------iaDAGKILSRMCFEANADWVTVICC-----------------------a 88 ::::::::::::::::::::::: d1iexa1 113 vglgatrdpylvkRIGEATALEVRATGIQYAFAPCIavcrdprwgrcyesysedrrivqs 172 d1q6oa_ 89 DINTAKGALD-----------vAKEF-NGDVQIEL-TGYW-------------------- 115 :::::::::: :::: :::::::: :::: d1iexa1 173 MTELIPGLQGdvpkdftsgmpfVAGKnKVAACAKHfVGDGgtvdginenntiinreglmn 232 d1q6oa_ 116 -TWEQAQQWRDAGIGQVVYHRSrdaqaaGVAWgeaDITAIK-RLSD---MGFKVTVT-GG 169 ::::::::::::::::::::: :::: :::::: :::: :::::::: :: d1iexa1 233 iHMPAYKNAMDKGVSTVMISYS----swNGVKmhaNQDLVTgYLKDtlkFKGFVISDwEG 288 d1q6oa_ 170 LA----------LEDLPLFKGIPIHVFIAGRsirdaaspveAARQFKRSIAELW------ 213 :: ::::::::::::::::::: ::::::::::::: d1iexa1 289 IDrittpagsdySYSVKASILAGLDMIMVPN----------KYQQFISILTGHVnggvip 338 d1q6oa_ 214 -------------------------------------------------- 214 d1iexa1 339 msriddavtrilrvkftmglfenpyadpamaeqlgkqehrdlareaarks 388 FAST alignment (Normalized score: 6.42 Raw score:1845.00) d1q6oa_ 1 LP-------------------------------MLQVALDNQTMDSAYET----TRLIAE 25 ::::: :::::: d1iexa1 1 --DYVLYKDATKPVEDRVADLLGRMTLAEKIGQMTQIE------------RLVATPDVLR 46 d1q6oa_ 26 --EVDIIEVGTILCVGEG------------VRAVRDLKALYP--------HKIVLADAKI 63 :::::::::: :::::::::: :::::::: d1iexa1 47 DNFIGSLLSGGG------SVPRKGATAKEWQDMVDGFQKA--CMSTRLGIPMIYGIDA-- 96 d1q6oa_ 64 AD------------------------------AGKILSRMCFEANADWVTVICCA----- 88 ::::::::::::::::: d1iexa1 97 --VHGQNNVYGATIFPHNVGLGATRDPYLVKRIGEATALEVRATGIQYA------FAPCI 148 d1q6oa_ 89 ------------------------DINTAKGALDVAKE------------------FNGD 106 :::::::: :::: d1iexa1 149 AVCRDPRWGRCYESYSEDRRIVQSMTELIPGL------QGDVPKDFTSGMPFVAGKNKVA 202 d1q6oa_ 107 VQIELTGYW----------------------------TWEQAQQWRDAGIGQVVYHRSRD 138 ::: :::::::::::::::::: d1iexa1 203 ACA------KHFVGDGGTVDGINENNTIINREGLMNIHMPAYKNAMDKGVSTVMI----- 251 d1q6oa_ 139 AQAAGVAWGEA------------DITAI-KRLSD---MGFKVTVTGGL------------ 170 ::::: ::::: ::::::::: d1iexa1 252 -----------SYSSWNGVKMHANQDLVTGYLKDTLKFKGFVISDW--EGIDRITTPAGS 298 d1q6oa_ 171 -ALEDLPLFKGIPIHVFIAGRSIRDAASPVEAARQFKRSIAELW---------------- 213 :::::::::::::::::::: ::::::::::: d1iexa1 299 DYSYSVKASILAGLDMIMVPN----------KYQQFISILTG--HVNGGVIPMSRIDDAV 346 d1q6oa_ 214 ------------------------------------------ 214 d1iexa1 347 TRILRVKFTMGLFENPYADPAMAEQLGKQEHRDLAREAARKS 388 TMalign alignment (TM-score: 0.71 Raw score:150.80) d1q6oa_ 1 ---------------------------LP--MLQVALDNQTMDSAYETTR-LIAE-E-VD 28 :: :::::: : ::: :::: : :: d1iexa1 1 DYVLYKDATKPVEDRVADLLGRMTLAEKIGQMTQIER-------L--VATPDVLRDNFIG 51 d1q6oa_ 29 IIEVGTILC--VGEGVR-AVRDLKALYP--H--------KIVLADAKI------------ 63 ::::::::: ::::: :::::::::: : ::::::::: d1iexa1 52 SLLSGGGSVPR-KGATAKEWQDMVDGFQKACMSTRLGIPMIYGIDAVHGQNNVYGATIFP 110 d1q6oa_ 64 -A-----------D--AGKILSRMCFEANADWVTVICC--------------A------- 88 : : :::::::::::::::::::::: : d1iexa1 111 HNVGLGATRDPYLVKRIGEATALEVRATGIQYAFAPCIAVCRDPRWGRCYESYSEDRRIV 170 d1q6oa_ 89 --DINTAKGALDV-----------AKEF-NGDVQIELT--GY------------------ 114 ::::::::::: :::: ::::::::: :: d1iexa1 171 QSMTELIPGLQGDVPKDFTSGMPFVAGKNKVAACAKHFVGDGGTVDGINENNTIINREGL 230 d1q6oa_ 115 --WTWEQAQQWRDAGIGQVVYHRSRDAQAAGVA-WGEAD--I-TAIK-RLSD-M-G-FKV 164 ::::::::::::::::::::: : :: :::: : :::: :::: : : ::: d1iexa1 231 MNIHMPAYKNAMDKGVSTVMISY---S----SWN-GVKMHANQDLVTGYLKDTLKFKGFV 282 d1q6oa_ 165 TVTGG-LA---------LE-DLPLFKGIPIHVFIAGRSIRDAASPVEAARQFKRSIA--E 211 ::::: :: :: :::::::::::::::: : :::::::::: : d1iexa1 283 ISDWEGIDRITTPAGSDYSYSVKASILAGLDMIMVP--N--------KYQQFISILTGHV 332 d1q6oa_ 212 ----L----W---------------------------------------------- 213 : : d1iexa1 333 NGGVIPMSRIDDAVTRILRVKFTMGLFENPYADPAMAEQLGKQEHRDLAREAARKS 388 HHsearch alignment (Probability: 0.29 E-value:0.02) d1q6oa_ 152 TAIKRLSDMGFKVTVTGG----------L-ALEDLPLFKGIPIHVFIAGRS 191 :::::::::::::::::: : ::::::::::::::::::::: d1iexa1 270 GYLKDTLKFKGFVISDWEGIDRITTPAGSDYSYSVKASILAGLDMIMVPNK 320