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: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1fw8a_ | Phosphoglycerate kinase | Phosphoglycerate kinase | Phosphoglycerate kinase | α/β |
| Hit | d1vc1a_ | Anti-sigma factor antagonist SpoIIaa | Anti-sigma factor antagonist SpoIIaa | SpoIIaa-like | α/β |
Query <-- 0.733 --> IntermediateDALI alignment (Z-score: 5.0 Raw score:484.70) query 1 ------------------------------------------------------------ 1 d1fw8a_ 1 skyslapvakelqsllgkdvtflndcvgpeveaavkasapgsvillenlryhieeegsrk 60 query 1 ------------------------------------------------------------ 1 d1fw8a_ 61 vdgqkvkaskedvqkfrhelssladvyindafgtahrahssmvgfdlpqraagfllekel 120 query 1 -------gMENKKMNLLLFS-GDYDKaLASLIIANAAremeiEVTIFCAFWGLL-LLRDp 51 :::::::::::: ::::: :::::::::: :::::::::::: :::: d1fw8a_ 121 kyfgkaleNPTRPFLAILGGaKVADK-IQLIDNLLDK-----VDSIIIGGGMAFtFKKV- 173 query 52 ekasqedkslyeqafSSLTPReAEELplskmnlggigkkmllemmkeekapKLSDLLSGA 111 :::::: :::: ::::::::: d1fw8a_ 174 ----------lenteIGDSIF-DKAG-----------------------aeIVPKLMEKA 199 query 112 RKKEVKFYAXQlsVEIM-------------gFKKE----elfpevqimDVKEYLKNALES 154 ::::::::::: :::: :::: :::::::::::: d1fw8a_ 200 KAKGVEVVLPV--DFIIadafsadantktvtDKEGipagwqgldngpeSRKLFAATVAKA 257 query 155 DLQLFI------------------------------------------------------ 160 :::::: d1fw8a_ 258 KTIVWNgppgvfefekfaagtkalldevvkssaagntviigggdtatvakkygvtdkish 317 query 161 ------------------------------------------------------------ 161 d1fw8a_ 318 vstgggaslellegkelpgvaflsekkslssklsvqdldlkdkrvfirvdfnvpldgkki 377 query 161 -------------------------------------- 161 d1fw8a_ 378 tsnqrivaalptikyvlehhpryvvlashlgrpngern 415 FAST alignment (Normalized score: 2.52 Raw score:648.60) query 1 GM---------------------------------------------------------- 2 d1fw8a_ 1 --SKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGS 58 query 3 ------------------------------------------------------------ 3 d1fw8a_ 59 RKVDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEK 118 query 3 -----------ENKKMNLLLFSGDYDKALASLIIANAAREMEIE---VTIFCAFWGLLLL 48 ::::::::::::::::::::::::: :::::::::: d1fw8a_ 119 ELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLL--------DKVDSIIIGGGMA--- 167 query 49 RDPEKASQEDKSLYEQAF-----------SSLTPREAEELPLSKMNLGGIGKKMLLEMMK 97 ::::: d1fw8a_ 168 ------------------FTFKKVLENTEIGDSI-------------------------- 183 query 98 EEKAP-------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIM-------- 142 :::::::::::::::::::: d1fw8a_ 184 -----FDKAGAEIVPKLMEKAKAKGVEVVLPV--------------------DFIIADAF 218 query 143 ---------------------------DVKEYLKNALESDLQLFI--------------- 160 :::::::::::::::: d1fw8a_ 219 SADANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKAKTIV--WNGPPGVFEFEKFAA 276 query 161 ------------------------------------------------------------ 161 d1fw8a_ 277 GTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPG 336 query 161 ------------------------------------------------------------ 161 d1fw8a_ 337 VAFLSEKKSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEH 396 query 161 ------------------- 161 d1fw8a_ 397 HPRYVVLASHLGRPNGERN 415 TMalign alignment (TM-score: 0.39 Raw score:62.58) query 1 ------------------------------------------------------------ 1 d1fw8a_ 1 SKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGSRK 60 query 1 ------------------------------------------------------------ 1 d1fw8a_ 61 VDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKEL 120 query 1 ---------GMENKKMNLLL-----------------------FS--------------- 13 :::::::::: :: d1fw8a_ 121 KYFGKALEN-PTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEI 179 query 14 ------------------------------------------------------------ 14 d1fw8a_ 180 GDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVTDKEGIPAGWQG 239 query 14 -GD-YDKALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTP 71 :: ::::::::::::::: :::::::::: : : : ::: d1fw8a_ 240 LDNGPESRKLFAATVAKAK----TIVWNGPPGV-F----------------E--F--EKF 274 query 72 REAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKK-EVKFYAXQLSVEIMGF 130 :::::: ::::::::::: :::::::::::: : d1fw8a_ 275 AAGTKA--------------------------LLDEVVKSSAAGNTVIIGGGDTAT---V 305 query 131 KKEELFPE-V--QI-MDVKEYLKNALE--------------------------------- 153 :::::::: : :: :::::::::::: d1fw8a_ 306 AKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKKSLSSKLSVQDLDLKDKRVFIR 365 query 154 --------------------------------------------------SDLQLFI 160 d1fw8a_ 366 VDFNVPLDGKKITSNQRIVAALPTIKYVLEHHPRYVVLASHLGRPNGERN------- 415 HHsearch alignment (Probability: 0.03 E-value:0.09) query 85 GGIGKKMLLEM---------MKEEKAPKLSDLLSGARKKEVKFY 119 ::::::::::: :::::::::::::::::::::::: d1fw8a_ 164 GGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVV 207
Intermediate <-- 0.759 --> HitDALI alignment (Z-score: 3.1 Raw score:281.10) d1fw8a_ 1 skyslapvakelqsllgkdvtflndcvgpeveaavkasapgsvillenlryhieeegsrk 60 d1vc1a_ 1 ------------------------------------------------------------ 1 d1fw8a_ 61 vdgqkvkaskedvqkfrhelssladvyindafgtahrahssmvgfdlpqraagfllekel 120 d1vc1a_ 1 ------------------------------------------------------------ 1 d1fw8a_ 121 kyfgkalenptrPFLAILGGA------kVADKIQLIDNLLDK--VDSIIIGGgmaftfkk 172 ::::::::: :::::::::::::: :::::::: d1vc1a_ 1 -mnnlkldiveqDDKAIVRVQgdidaynSSELKEQLRNFISTtsKKKIVLDL-------- 51 d1fw8a_ 173 vlenteigdSIFDKAGAEIVPKLMEKAKAKGVEVVL-PVDFiiadafsadantktvtdke 231 ::::::::::::::::::::::::::: :::: d1vc1a_ 52 ------ssvSYMDSAGLGTLVVILKDAKINGKEFILsSLKE-----------------si 88 d1fw8a_ 232 gipagwqgldngpesRKLFAATvakaktivwngppgvfefekfaagtkalldevvkssaa 291 ::::::: d1vc1a_ 89 srilklthldkifkiTDTVEEA-------------------------------------- 110 d1fw8a_ 292 gntviigggdtatvakkygvtdkishvstgggaslellegkelpgvaflsekkslsskls 351 d1vc1a_ 111 ------------------------------------------------------------ 111 d1fw8a_ 352 vqdldlkdkrvfirvdfnvpldgkkitsnqrivaalptikyvlehhpryvvlashlgrpn 411 d1vc1a_ 111 ------------------------------------------------------------ 111 d1fw8a_ 412 gern 415 d1vc1a_ 111 ---- 111 FAST alignment (Normalized score: 2.56 Raw score:548.10) d1fw8a_ 1 SKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGSRK 60 d1vc1a_ 1 ------------------------------------------------------------ 1 d1fw8a_ 61 VDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKEL 120 d1vc1a_ 1 ------------------------------------------------------------ 1 d1fw8a_ 121 KYFGKALENPTR------------PFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAF 168 :::::: d1vc1a_ 1 ------------MNNLKLDIVEQDDKAIVR------------------------------ 18 d1fw8a_ 169 TFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT 228 d1vc1a_ 19 ------------------------------------------------------------ 19 d1fw8a_ 229 DKEGIPAGWQGLDN---------GPESRKLFAATVAK--AKTIVWNGPPGVFEFEK---- 273 :::::::::::::: :::::: d1vc1a_ 19 --------------VQGDIDAYNSSELKEQLRNFISTTSKKKIVL-----------DLSS 53 d1fw8a_ 274 ----FAAGTKALLDEVVKSSAAGNTVIIG--GGDTATVAKKYGVTDKISHVSTGGGASLE 327 ::::::::::::::::::::::::: ::::::::::::::::: d1vc1a_ 54 VSYMDSAGLGTLVVILKDAKINGKEFILSSLKESISRILKLTHLDKIF------------ 101 d1fw8a_ 328 LLEGKELPGVAFLSEKKSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAAL 387 d1vc1a_ 102 ------------------------------------------------------------ 102 d1fw8a_ 388 PTIKYVLEHHPRYVVLASHLGRPNGERN--------- 415 d1vc1a_ 102 ----------------------------KITDTVEEA 110 TMalign alignment (TM-score: 0.17 Raw score:69.31) d1fw8a_ 1 --------SKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYH 52 d1vc1a_ 1 MNNLKLDI---------------------------------------------------- 8 d1fw8a_ 53 IEEEGSRKVDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAA 112 d1vc1a_ 9 ------------------------------------------------------------ 9 d1fw8a_ 113 GFLLEKELKYFGKALENPTRPFLAILGGAKV----A-DKIQLIDNLLDKV--DSIIIGG- 164 : :::::::::::::: : ::::::::::::: ::::::: d1vc1a_ 9 -------------V---EQDDKAIVRVQGDIDAYNSSELKEQLRNFISTTSKKKIVLDLS 52 d1fw8a_ 165 -GMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIA-DAFSADA 222 : ::::::::::::::::::::::::::::::: :: d1vc1a_ 53 SV----------------SYMDSAGLGTLVVILKDAKINGKEFILSSLK-ESI------- 88 d1fw8a_ 223 NTKTVTDKEGI------------PAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFE 270 : :: ::: :::: d1vc1a_ 89 ------S--RILKLTHLDKIFKI-----------TDT--VEEA----------------- 110 d1fw8a_ 271 FEKFAAGTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLE 330 d1vc1a_ 111 ------------------------------------------------------------ 111 d1fw8a_ 331 GKELPGVAFLSEKKSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTI 390 d1vc1a_ 111 ------------------------------------------------------------ 111 d1fw8a_ 391 KYVLEHHPRYVVLASHLGRPNGERN 415 d1vc1a_ 111 ------------------------- 111 HHsearch alignment (Probability: 0.01 E-value:0.45) d1fw8a_ 240 LDNGPESRKLFAATVA--KAKTIVWNGPPGVFEFEKFAAGTKALLDEVVKSSAAG-NTVI 296 :::::::::::::::: :::::::::::::::: :::::::::::::::::: :::: d1vc1a_ 25 AYNSSELKEQLRNFISTTSKKKIVLDLSSVSYMD---SAGLGTLVVILKDAKINGKEFIL 81 d1fw8a_ 297 IG-GGDTATVAKKYGVTDKISHVST 320 :: :::::::::::::::::::::: d1vc1a_ 82 SSLKESISRILKLTHLDKIFKITDT 106