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 | d1saya1 | L-alanine dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
| Hit | d1f0ka_ | Peptidoglycan biosynthesis glycosyltransferase MurG | UDP-Glycosyltransferase/glycogen phosphorylase | UDP-Glycosyltransferase/glycogen phosphorylase | α/β |
Query <-- 0.833 --> IntermediateDALI alignment (Z-score: 4.0 Raw score:377.80) query 1 ----------------------GMEN------KKMNLLLfsgdydkALASLIIANAAREM 32 :::: ::::::: :::::::::::::: d1saya1 1 agrlsvqfgarflerqqggrgvLLGGvpgvkpGKVVILG------gGVVGTEAAKMAVGL 54 query 33 EIEVTIFCAfwGLLLLRdpekasqedkslyeqafssltpreaeelplskmnlggigkkml 92 ::::::::: :::::: d1saya1 55 GAQVQIFDI--NVERLS------------------------------------------- 69 query 93 lemmkeekapklsdlLSGARkkEVKFYAXqlsveimgfkkeelfpevqimDVKEYLKNAL 152 ::::: ::::::: :::::::::: d1saya1 70 -------------ylETLFG-sRVELLYS---------------------NSAEIETAVA 94 query 153 ESDLQLFI---------------------------------------------------- 160 :::::::: d1saya1 95 EADLLIGAvlvpgrrapilvpaslveqmrtgsvivdvavdqggcvetlhptshtqptyev 154 query 161 -------------- 161 d1saya1 155 fgvvhygvpnmpga 168 FAST alignment (Normalized score: 3.98 Raw score:652.10) query 1 GME-------------------------------NKKMNLLLFSGDYDK---ALASLIIA 26 :::::: :::::::: d1saya1 1 ---AGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVI---------LGGGVVGTEAA 48 query 27 NAAREMEIEVTIFCAFW-GLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLG 85 :::::::::::::: :::: d1saya1 49 KMAVGLGAQVQIFD---INVER-------------------------------------- 67 query 86 GIGKKMLLEMMKEEKAPKLSDLLS--GARKK----EVKFYAXQLSVEIMGFKKEELFPEV 139 :::: :::::: d1saya1 68 ------------------------LSYLET-LFGSRVELLY------------------- 83 query 140 QIMDVKEYLKNALESDLQLFI--------------------------------------- 160 ::::::::::::::::: d1saya1 84 --SNSAEIETAVAEADLLI--GAVLVPGRRAPILVPASLVEQMRTGSVIVDVAVDQGGCV 139 query 161 ----------------------------- 161 d1saya1 140 ETLHPTSHTQPTYEVFGVVHYGVPNMPGA 168 TMalign alignment (TM-score: 0.40 Raw score:63.78) query 1 ----------------------GME------NKKMNLLLFSGDYDKALASLIIANAAREM 32 ::: :::::::: ::::::::::::::: d1saya1 1 AGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVILG------GGVVGTEAAKMAVGL 54 query 33 EIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKML 92 ::::::::: :::::: : d1saya1 55 GAQVQIFDI--NVERLS------------------------Y------------------ 70 query 93 LEMMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNAL 152 ::::::: ::::::: :::::::::: d1saya1 71 --------------LETLFGS-RVELLYS---------------------NSAEIETAVA 94 query 153 ESDLQLF-I--------------------------------------------------- 160 ::::::: : d1saya1 95 EADLLIGAVLVPGRRAPILVPASLVEQMRTGSVIVDVAVDQGGCVETLHPTSHTQPTYEV 154 query 161 -------------- 161 d1saya1 155 FGVVHYGVPNMPGA 168 HHsearch alignment (Probability: 0.08 E-value:0.01) query 21 ASLIIANAAREMEIEVTIF 39 ::::::::::::::::::: d1saya1 43 VGTEAAKMAVGLGAQVQIF 61
Intermediate <-- 1.304 --> HitDALI alignment (Z-score: 6.3 Raw score:530.40) d1saya1 1 ------------------------------------------------------------ 1 d1f0ka_ 1 krlmvmaggtgghvfpglavahhlmaqgwqvrwlgtadrmeadlvpkhgieidfirisgl 60 d1saya1 1 ------------------------------------------------------------ 1 d1f0ka_ 61 rgkgikaliaaplrifnawrqaraimkaykpdvvlgmggyvsgpgglaawslgipvvlhe 120 d1saya1 1 -------------------------agrlsvqfgarflerqqggrgvllggvpgVKPGKV 35 :::::: d1f0ka_ 121 qngiagltnkwlakiatkvmqafpgafpnaevvgnpvrtdvlalplpqqrlagrEGPVRV 180 d1saya1 36 VILG---GGVVGTEAAKMAVGLG---AQVQIFDINvERLSYLETLFG----SRVELL-YS 84 :::: :::::::::::::::: ::::::::: ::::::::::: :::::: :: d1f0ka_ 181 LVVGgsqGARILNQTMPQVAAKLgdsVTIWHQSGK-GSQQSVEQAYAeagqPQHKVTeFI 239 d1saya1 85 NSaeIETAVAEADLLIGAvlvpgrrAPIL--VPASLVeqmrtgSVIVDVA----vDQGGc 138 :: :::::::::::::: :::: :::::: ::::::: :::: d1f0ka_ 240 DD--MAAAYAWADVVVCR------sGALTvsEIAAAG------LPALFVPfqhkdRQQY- 284 d1saya1 139 veTLHPtshtqpTYEVfgvVHYGVPNMP-------------------------------- 166 :::: :::: ::::::::: d1f0ka_ 285 -wNALP-----lEKAG---AAKIIEQPQlsvdavantlagwsretlltmaeraraasipd 335 d1saya1 167 --------------ga 168 d1f0ka_ 336 atervanevsrvaral 351 FAST alignment (Normalized score: 2.99 Raw score:725.90) d1saya1 1 AGRLSVQFGARFLERQQGGRGVLLGGVPG------------------------------- 29 d1f0ka_ 1 -----------------------------KRLMVMAGGTGGHVFPGLAVAHHLMAQGWQV 31 d1saya1 30 ------------------------------------------------------------ 30 d1f0ka_ 32 RWLGTADRMEADLVPKHGIEIDFIRISGLRGKGIKALIAAPLRIFNAWRQARAIMKAYKP 91 d1saya1 30 ------------------------------------------------------------ 30 d1f0ka_ 92 DVVLGMGGYVSGPGGLAAWSLGIPVVLHEQNGIAGLTNKWLAKIATKVMQAFPGAFPNAE 151 d1saya1 30 -----------------------VKPGKVVILG-----GGVVGTEAAKMAVG---LGAQV 58 :::::::: :::::::::::::: ::::: d1f0ka_ 152 VVGNPVRTDVLALPLPQQRLAGREGPVRVLV--VGGSQGARILNQTMPQVAAKLGDSVTI 209 d1saya1 59 QIFDINVERLSYLETLFG------SRVELLYSNSA----EIETAVAEADLLIGAVLVPGR 108 :::: ::::::::::: :::::: :::::::::::: d1f0ka_ 210 WHQS-GKGSQQSVEQA--YAEAGQPQHKVT-----EFIDDMAAAYAWADVV--------- 252 d1saya1 109 RAPIL---VPASLVEQMR---TGSVIVDVAVDQGGCVETLHPTSHTQPTYEVFGV----- 157 :::::::: ::::::: d1f0ka_ 253 -----VCRSGALTVSE--IAAAGLPALF---------------------------VPFQH 278 d1saya1 158 ----------------VHYGVPNMPGA--------------------------------- 168 ::::: d1f0ka_ 279 KDRQQYWNALPLEKAGAAKII------EQPQLSVDAVANTLAGWSRETLLTMAERARAAS 332 d1saya1 169 ------------------- 169 d1f0ka_ 333 IPDATERVANEVSRVARAL 351 TMalign alignment (TM-score: 0.53 Raw score:89.67) d1saya1 1 ------------------------------------------------------------ 1 d1f0ka_ 1 KRLMVMAGGTGGHVFPGLAVAHHLMAQGWQVRWLGTADRMEADLVPKHGIEIDFIRISGL 60 d1saya1 1 ------------------------------------------------------------ 1 d1f0ka_ 61 RGKGIKALIAAPLRIFNAWRQARAIMKAYKPDVVLGMGGYVSGPGGLAAWSLGIPVVLHE 120 d1saya1 1 -----------------------------------------------AGRLSVQFGARFL 13 d1f0ka_ 121 QNGIAGLTNKWLAKIATKVMQAFPGAFPNAEVVGNPVRTDVLALPLP------------- 167 d1saya1 14 ERQQGGR------GVLLGGVPGVKPGKVVILG----GGVVGTEAAKMAVGL-G-AQVQIF 61 : :::::::::: ::::::::::::::: : :::::: d1f0ka_ 168 ------QQRLAGR---------EGPVRVLVVGGSQGARILNQTMPQVAAKLGDSVTIWHQ 212 d1saya1 62 DINVERLSYLETLFG----SRVELLYSNSAEIETAVAEADLLIGAVLVPGRRAPILVPAS 117 ::: ::::::::::: ::::::::::: ::::::::::::::: ::: :::: d1f0ka_ 213 SGK-GSQQSVEQAYAEAGQPQHKVTEFIDD-MAAAYAWADVVVCRS------GAL-TVSE 263 d1saya1 118 LVEQMRTGSVIVDVAVD---QGGCVETLHPTSHTQPTYEVFGVVHYGVP-NMPG--A--- 168 ::::: ::::::::: ::: ::::::: ::: ::::::: :::: : d1f0ka_ 264 IAAAG---LPALFVPFQHKDRQQ-YWNALPL-----EKA---GAAKIIEQPQLSVDAVAN 311 d1saya1 169 ---------------------------------------- 169 d1f0ka_ 312 TLAGWSRETLLTMAERARAASIPDATERVANEVSRVARAL 351 HHsearch alignment (Probability: 0.91 E-value:0.00) d1saya1 33 GKVVILGGG----VVGTEAAKMAVGLGAQVQIF----DINVERLSYLETLFGSRVELLYS 84 ::::::::: :::::::::::::::::::: ::::::::::::::::::::::: d1f0ka_ 178 VRVLVVGGSQGARILNQTMPQVAAKLGDSVTIWHQSGKGSQQSVEQAYAEAGQPQHKVTE 237 d1saya1 85 NSAEIETAVAEADLLIGAVLVPGRRAPILVPASLVEQMRTGSVIVDV 131 :::::::::::::::::: ::::: : :: ::::::::::::: d1f0ka_ 238 FIDDMAAAYAWADVVVCR---SGALT---V-SE-IAAAGLPALFVPF 276