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 <-- 0.727 --> Intermediate <-- 0.596 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1qwna3) through the intermediate protein (d1u1ja1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1u1ja1 5-​methyltetrahydropteroyltriglutamate-​-​homocysteine methyltransferase MetEUROD/​MetE-​likeTIM beta/​alpha-​barrelα/β
Hit d1qwna3 Golgi alpha-​mannosidase IIGlycoside hydrolase/​deacetylase7-​stranded beta/​alpha barrelα/β

Supporting Alignments

Query <-- 0.727 --> Intermediate
DALI alignment (Z-score: 5.6 Raw score:745.20) query 1 ----------------------mIETPY--YLIDKAKLTRNMERIAHVREkSGAK-ALLA 35 ::::: :::::::::::::::::::: :::: :::: d1u1ja1 1 ashivgyprmgpkrelkfalesfWDGKStaEDLQKVSADLRSSIWKQMSA-AGTKfIPSN 59 query 36 L----------------------------------------------------------- 36 : d1u1ja1 60 Tfahydqvldttamlgavpprygytggeigldvyfsmargnasvpamemtkwfdtnyhyi 119 query 37 -----------kcfATWSVF-DLMR--DYMDGTTSSSL---------------------- 60 :::::: :::: ::::::::::: d1u1ja1 120 vpelgpevnfsyasHKAVNEyKEAKalGVDTVPVLVGPvsylllskaakgvdksfellsl 179 query 61 -----fevrlgRERF----GKETHAYSVAY-----------GDNEIDE----vvsHADKI 96 :::: ::::::::::: ::::::: ::::: d1u1ja1 180 lpkilpiykevITELkaagATWIQLDEPVLvmdlegqklqaFTGAYAElestlsgLNVLV 239 query 97 IF--NSIS--QLERFADKaagIARGLRLNpqrLGEWdVPKVERVMD--riNGFMI-HNNC 149 :: :::: :::::::: :::::::: :::: ::::::::: ::::: :::: d1u1ja1 240 ETyfADIPaeAYKTLTSLkgvTAFGFDLV---RGTKtLDLVKAGFPegkyLFAGVvDGRN 296 query 150 enkdfglfdRMLGeiEERFGALIARV--------DWVSL--GGGI-------------hf 186 :::: ::::::::::: ::::: :::: d1u1ja1 297 --------iWAND--FAASLSTLQALegivgkdkLVVSTscSLLHtavdlinetklddei 346 query 187 tgddypvdafSARLRAFSDRYGvqiylepgeasitksttlevtvldtlynknlaivdssi 246 :::::::::::: d1u1ja1 347 kswmafaaqkVVEVNALAKALA-------------------------------------- 368 query 247 eahmldlliyretakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaag 306 d1u1ja1 369 ------------------------------------------------------------ 369 query 307 ytmvkknwfngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1u1ja1 369 ----------------gqkdealfsanaaalasrrssprvtn 394 FAST alignment (Normalized score: 3.68 Raw score:1364.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFA-------------------- 40 :::: d1u1ja1 1 ------------------------------ASHI------VGYPRMGPKRELKFALESFW 24 query 41 ----------------TWSVFDLMRD-YMDGTTSS------------------------- 58 :::::::::: :::::: d1u1ja1 25 DGKSTAEDLQKVSADLRSSIWKQMSAAGTKFIP--SNTFAHYDQVLDTTAMLGAVPPRYG 82 query 59 -----------------------------------------------------SLFEVRL 65 ::::::: d1u1ja1 83 YTGGEIGLDVYFSMARGNASVPAMEMTKWFDTNYHYIVPELGPEVNFSYASHKAVNEYKE 142 query 66 GRERFGKETHAYSVAY--------------------------------GDNEIDEVVS-H 92 ::: ::::::::: :::::::::: : d1u1ja1 143 AKA-LGVDTVPVL---VGPVSYLLLSKAAKGVDKSFELLSLLPKILPIYKEVITELKAAG 198 query 93 ADKIIFN----------------SISQLERFADKAAGIARGLRLNPQRLGE----WDVPK 132 :::::: ::::::::::::::::::::: ::::: d1u1ja1 199 ATWIQL-DEPVLVMDLEGQKLQAFTGAYAELESTLSGLNVLVET-------YFADIPAEA 250 query 133 VERVM--DRINGFMIHNNCENKDFGLFDRML---GEIEERFGALIARV-----DWVSLGG 182 ::::: :::::::::: ::::::::: ::::: d1u1ja1 251 YKTLTSLKGVTAFGFDL--------------VRGTKTLDLVKA-----GFPEGKYLFA-- 289 query 183 GIHFTG--------DDYPVDAFSARLRAFSDRYGV----QIYL----EPGEASITKSTTL 226 :::::::::::::::::: :::: :::: d1u1ja1 290 ------GVVDGRNIWANDFAASLSTLQALEGI---VGKDKLVVSTSCSLLH--------- 331 query 227 EVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGE 286 d1u1ja1 332 ------------------------------------------------------------ 332 query 287 FRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQS 346 d1u1ja1 332 ------------------------------------------------------------ 332 query 347 LS---------------------------------------------------------- 348 d1u1ja1 332 --TAVDLINETKLDDEIKSWMAFAAQKVVEVNALAKALAGQKDEALFSANAAALASRRSS 389 query 349 ----- 349 d1u1ja1 390 PRVTN 394 TMalign alignment (TM-score: 0.44 Raw score:152.83) query 1 ----------------------MIETPY--YLI-DKAKLTRNMER-IAHVREKSGAKALL 34 :::: ::: ::::::::::: :::::::::::::: d1u1ja1 1 ASHIVGYPRMGPKRELKFALES--FWDGKSTAEDLQKVSADLRSSIWKQMSAAGTKFIPS 58 query 35 AL----KC--FA------------------------------------------------ 40 :: :: :: d1u1ja1 59 NTFAHYDQVLDTTAMLGAVPPRYGYTGGEIGLDVYFSMARGNASVPAMEMTKWFDTNYHY 118 query 41 --------------TWS--VF-DLMRD--YMDGTTSSSL--------------------- 60 ::: :: ::::: :::::::::: d1u1ja1 119 IVPELGPEVNFSYASHKAVNEYKEAKALGVDTVPVLVGPVSYLLLSKAAKGVDKSFELLS 178 query 61 ----F--EVRLGRERFG---K-ETHAYS-VA--------Y-G-DNEIDEVV-SH--ADKI 96 : :::::::::: : :::::: :: : : :::::::: :: :::: d1u1ja1 179 LLPKILPIYKEVITELKAAGATWIQLDEPVLVMDLEGQKLQAFTGAYAELESTLSGLNVL 238 query 97 IFN----S-ISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDR-INGFMI-HNNC 149 ::: : ::::::::::: ::::::::::: :::::::::::::: :::::: :::: d1u1ja1 239 VETYFADIPAEAYKTLTSLK-GVTAFGFDLVR--GTKTLDLVKAGFPEGKYLFAGVVDGR 295 query 150 ENKDFGLFDRMLGEIEERFGALIA--R--VDWVSL-GGGI-HFTGDDY------------ 191 : : : :::::::::::::::: : :::::: :::: ::::::: d1u1ja1 296 -N-I--W-ANDFAASLSTLQALEGIVGKDKLVVSTSCSLLHTAVDLINETKLDDEIKSWM 350 query 192 -PVDAFSARLRAFSDRYGV-------------------------QIYLEPGEASITKSTT 225 :::::::::::::::::: d1u1ja1 351 AFAAQKVVEVNALAKALAGQKDEALFSANAAALASRRSSPRVTN---------------- 394 query 226 LEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFG 285 d1u1ja1 395 ------------------------------------------------------------ 395 query 286 EFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQ 345 d1u1ja1 395 ------------------------------------------------------------ 395 query 346 SLS 348 d1u1ja1 395 --- 395 HHsearch alignment (Probability: 0.15 E-value:0.00) query 2 IETPYYLID-----KAKLTRNMERIAHVREKSGAK--ALL-ALKCFATWSVFDLMRDYMD 53 ::::::::: ::::::::::::::::::::: ::: ::::::::::::::::::: d1u1ja1 204 LDEPVLVMDLEGQKLQAFTGAYAELESTLSGLNVLVETYFADIPAEAYKTLTSLKGVTAF 263 query 54 GTTSSSLFEVRLGRERFGKETHAYSVA 80 ::::::::::::::::::::::::::: d1u1ja1 264 GFDLVRGTKTLDLVKAGFPEGKYLFAG 290
Intermediate <-- 0.596 --> Hit
DALI alignment (Z-score: 4.3 Raw score:677.60) d1u1ja1 1 -----------------------------------------------------ASHIVG- 6 :::::: d1qwna3 1 cqdvvqdvpnvdvqmlelydrmsfkdidggvwkqgwnikydplkynahhklkvFVVPHSh 60 d1u1ja1 7 --------------yPRMGpkrelkfalesfwdgkstaedlqkvsaDLRSSIWKQmSAAG 52 :::: ::::::::: :::: d1qwna3 61 ndpgwiqtfeeyyqhDTKH-------------------------ilSNALRHLHD-NPEM 94 d1u1ja1 53 tkfIPSNtfahydqvldttamlgavpprygytggeigldvyfsmargnasvpamemtkwf 112 :::: d1qwna3 95 --kFIWA----------------------------------------------------- 99 d1u1ja1 113 dtnyhyivpelgpevnfsyasHKAV-----------neyKEAKAlGVDTVPVL----VGP 157 :::: ::::: :::::::: ::: d1qwna3 100 -------------------eiSYFArfyhdlgenkklqmKSIVK-NGQLEFVTggwvMPD 139 d1u1ja1 158 VsylllskaakgvdksfelLSLLPKILPIYKEVITELKA-AGAT-wiqLDEPVLvmdleg 215 : :::::::::::::::::::: :::: :::::: d1qwna3 140 E-----------------aNSHWRNVLLQLTEGQTWLKQfMNVTptasWAIDPF------ 176 d1u1ja1 216 qklqaFTGAYAELESTlSGLNVLVEtyfadIPAEAY------ktlTSLK----------- 258 ::::::::::: :::::::: :::::: :::: d1qwna3 177 ---ghSPTMPYILQKS-GFKNMLIQ----rTHYSVKkelaqqrqlEFLWrqiwdnkgdta 228 d1u1ja1 259 GVTAFG----FDLVRgtktldlvkagfpegkylfagvvdgrNIWA--------------- 299 :::::: ::::: :::: d1qwna3 229 LFTHMMpfysYDIPH-------------tcgpdpkvccqfdFKRMgsfglscpwkvpprt 275 d1u1ja1 300 -------nDFAASLSTLQALEGIVgKDKLVVSTsCSLLH-tAVDLinetklddeikswma 351 :::::::::::::::: :::::::: ::::: :::: d1qwna3 276 isdqnvaaRSDLLVDQWKKKAELYrTNVLLIPL-GDDFRfkQNTE--------------- 319 d1u1ja1 352 fAAQKVVEVNALAKAlagQKDEA-----------------------lfsanaaalasrrs 388 :::::::::::::: ::::: d1qwna3 320 -WDVQRVNYERLFEH---INSQAhfnvqaqfgtlqeyfdavhqaeragqaefptlsgdff 375 d1u1ja1 389 sprvtn 394 d1qwna3 376 tyadrs 381 FAST alignment (Normalized score: 2.12 Raw score:820.30) d1u1ja1 1 -----------------------------------------------------ASHIVGY 7 :::: d1qwna3 1 CQDVVQDVPNVDVQMLELYDRMSFKDIDGGVWKQGWNIKYDPLKYNAHHKLKVFVVP--- 57 d1u1ja1 8 PRMGPKRELKFALESFWDGKSTA----------------EDLQKVSADLRSSIWKQMSAA 51 ::::::::::::::::: d1qwna3 58 -----------------------HSHNDPGWIQTFEEYYQHDTKHILSNALRHLHD---- 90 d1u1ja1 52 GT---KFIPSNTFAHYDQVLDTTAMLGAVPPRYGYTGGEIGLDVYFSMARGNASVPAMEM 108 :::: d1qwna3 91 --NPEMKFI--------------------------------------------------- 97 d1u1ja1 109 TKWFDTNYHYIVPELGPEVNFSYASHK--AVNEYKEAKALGV------------------ 148 ::::::::: d1qwna3 98 ---------------------------WAEISYFARFY----HDLGENKKLQMKSIVKNG 126 d1u1ja1 149 DTVPVLVGPVSYLLLSKAAKGVDKSFELLS-------------LLPKILPIYKEVITELK 195 :::: ::::::::::::::::: d1qwna3 127 QLEF--------------------------VTGGWVMPDEANSHWRNVLLQLTEGQTWLK 160 d1u1ja1 196 AAGATW------IQLDEPVLVMDLEGQKLQA-----FTGAYAELESTLSGLNVLVETYFA 244 : :::::: :::::::::: ::: :::::: d1qwna3 161 Q-----FMNVTPTASWAI-------------DPFGHSPTMPYILQK--SGF-KNMLIQ-- 197 d1u1ja1 245 DIPAEAYKTLTSLKGV-------------------------------TAFGFDLVRGTKT 273 ::::::: d1qwna3 198 ----------------RTHYSVKKELAQQRQLEFLWRQIWDNKGDTALFTHMMP------ 235 d1u1ja1 274 LDLVKAGFPEGKYLFAGVVDGRNIWAN--------------------------------- 300 d1qwna3 236 ---------------------------FYSYDIPHTCGPDPKVCCQFDFKRMGSFGLSCP 268 d1u1ja1 301 ---------------DFAASLSTLQALEGIVG---KDKLVVSTSCSLLHTAVDLINETKL 342 :::::::::::::: :::::: d1qwna3 269 WKVPPRTISDQNVAARSDLLVDQWKKKAE---LYRTNVLLI------------------- 306 d1u1ja1 343 DDEIKSWMA------------FAAQKVVEVNALAKALAGQKDEALFSANAAALASRRSSP 390 :::::::::::::::: d1qwna3 307 ---------PLGDDFRFKQNTEWDVQRVNYERLFEHI----------------------- 334 d1u1ja1 391 RVTN----------------------------------------------- 394 d1qwna3 335 ----NSQAHFNVQAQFGTLQEYFDAVHQAERAGQAEFPTLSGDFFTYADRS 381 TMalign alignment (TM-score: 0.41 Raw score:162.21) d1u1ja1 1 -----------------------------------------------------ASHIVGY 7 ::::::: d1qwna3 1 CQDVVQDVPNVDVQMLELYDRMSFKDIDGGVWKQGWNIKYDPLKYNAHHKLKVFVVPHSH 60 d1u1ja1 8 PR-------MGPKRELK-FALE-SFWDGKSTAEDLQKVSADLRSSIWKQMSAAGTKFIPS 58 :: :: ::: :: :::::::::::: :: :: :::: d1qwna3 61 NDPGWIQTF------EEY-YQHD-----------TK-HILSNALRHLHD-NP-EM-KFIW 98 d1u1ja1 59 NTFAHYDQVLDTTAMLGAVPPRYGYTGGEIGLDVYFSMARGNASVPAMEMTKWFDTNYHY 118 : : :: :: ::: d1qwna3 99 A------E--IS-YF--------------ARF---------------------------- 107 d1u1ja1 119 IVPELGPEVNFSYASHK--AVN-EYKEAKAL-GVD-TVPVLVGPVSYLLLSKAAKGVDKS 173 ::: : :::::::: ::: ::::::::::::: d1qwna3 108 --------------YHDLG--ENKKLQMKSIVKNGQLEFVTGGWVMPDE----------- 140 d1u1ja1 174 FELLSLLPKILPIYKEVITELKA--AGATWIQLDEPVLVMDLEGQKLQAFTGAYAELEST 231 ::::::::::::::::::::: ::::::::::::: : : ::::::::::: d1qwna3 141 --ANSHWRNVLLQLTEGQTWLKQFMNVTPTASWAIDPF---G----H--SPTMPYILQKS 189 d1u1ja1 232 LSGLNVLVETYFADIPAEAY-K----TLTS-L----------KGVTAFGF---DLVRGTK 272 :: : :::::: ::::::: : :::: : :::::::: ::::::: d1qwna3 190 GF-K-NMLIQR--THYSVKKELAQQRQLEFLWRQIWDNKGDTALFTHMMPFYSYDIPHTC 245 d1u1ja1 273 TLD---LVKAGFPEGKYLFAGVVDGRNI-----------WAN---------DFAASLSTL 309 ::: ::::::::: ::: ::::::::: d1qwna3 246 GPDPKV-------------CCQFDFKRMGSFGLSCPWKVPPRTISDQNVAARSDLLVDQW 292 d1u1ja1 310 QALEGIVGKDKLVVSTSCSLLHTAVDLINETKLDDEIKSWMAFAAQKVVEVNALAKALAG 369 :::::::::::::::: :::::::::: :::::::::::::::: : d1qwna3 293 KKKAELYRTNVLLIPL-GDDFRFKQNT---------------EWDVQRVNYERLFEHI-N 335 d1u1ja1 370 QKDE------------------------------------------ALFSANAAALASRR 387 :::: d1qwna3 336 SQAHFNVQAQFGTLQEYFDAVHQAERAGQAEFPTLSGDFFTYADRS-------------- 381 d1u1ja1 388 SSPRVTN 394 d1qwna3 382 ------- 382 HHsearch alignment (Probability: 0.09 E-value:0.52) d1u1ja1 180 LPKILPIYKEVITELKAA------GATWIQLDEPVLVMDLEG-QKLQAFTGAYAELESTL 232 :::::::::::::::::: :::::::::::::::::: :::::::::::::::: d1qwna3 108 YHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTEGQTWLKQFMNVT- 166 d1u1ja1 233 SGLNVLVETYFADIPAEAYKTLTSLKGVTAFGFD 266 :: ::::::::::: :::::::::::::::::: d1qwna3 167 PT-ASWAIDPFGHS--PTMPYILQKSGFKNMLIQ 197