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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1ujpa_ | Trp synthase alpha-subunit | Ribulose-phoshate binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1qv9a_ | F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) | F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) | F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) | α/β |
Query <-- 1.022 --> IntermediateDALI alignment (Z-score: 9.2 Raw score:936.30) query 1 mietpyylidkakltrnmeriahvrEKSGAKALLALK-----cfaTWSVFDLMRDYMDGT 55 :::::::::::: ::::::::::::::: d1ujpa_ 1 --------------mttleafakarSEGRAALIPYLTagfpsregFLQAVEEVLPYADLL 46 query 56 TSSS-------------------------LFEVRLGRERFGKETHAYSVA------yGDN 84 :::: ::::::::::::::::::::: ::: d1ujpa_ 47 EIGLpysdgpviqraselalrkgmsvqgaLELVREVRALTEKPLFLMTYLnpvlawgPER 106 query 85 EIDEVVS-HADKIIF-NSIS-qlERFADKAA--GIARGLRLNPQrlgeWDVPKVERVMDR 139 ::::::: ::::::: :::: :::::::: ::::::::::: :::::::::::: d1ujpa_ 107 FFGLFKQaGATGVILpDLPPdedPGLVRLAQeiGLETVFLLAPT----STDARIATVVRH 162 query 140 IN-GFMIHNNcenkdfglfdrMLGEIEERFGALIArvDWVSLGGGIHFtgddypvDAFSA 198 :: ::::::: :::::::::::::: ::::::::::: ::::: d1ujpa_ 163 ATgFVYAVSV-----------EVKDLVRRIKARTA--LPVAVGFGVSG-------KATAA 202 query 199 RLRafsdrygvqIYLEPGEASI-TKSTtlevtvldtlynknlaivdssieahmldlliyr 257 ::: :::::::::: :::: d1ujpa_ 203 QAA-------vaDGVVVGSALVrALEE--------------------------------- 222 query 258 etakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqDAAGytmvkknwfng 317 :::: d1ujpa_ 223 ---------------------------------------------GRSL----------- 226 query 318 vkmpaiaireldgsvrtvreftyadyeqsls 348 d1ujpa_ 227 --------------apllqeirqglqrlplp 243 FAST alignment (Normalized score: 5.49 Raw score:1595.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS--------------GAKALLALKCFA------ 40 ::::::: d1ujpa_ 1 ----------------------------MTTLEAFAKARSEGRAALIPY-----LTAGFP 27 query 41 ----TWSVFDLMRDYMDGTTSS--------------------------SLFEVRLGRERF 70 ::::::::::::::::: :::::::::::: d1ujpa_ 28 SREGFLQAVEEVLPYADLLEI-GLPYSDGPVIQRASELALRKGMSVQGALELVREVRALT 86 query 71 GKETHAYSVAY---------GDNEIDEVVS-HADKIIFNSIS--QLERFADKA-----AG 113 :::::::: :::::::::: :::::::: ::::::::: :: d1ujpa_ 87 EKPLFLMT---YLNPVLAWGPERFFGLFKQAGATGVILP---DLPPDEDPGLVRLAQEIG 140 query 114 IARGLRLNPQRLGE-WDVPKVERVMDR-INGFMIHNNCENKDFG--LFDRMLGEIEERFG 169 ::::::::: :::::::::::: ::::::: :::::::::::: d1ujpa_ 141 LETVFLLAP-----TSTDARIATVVRHATGFVYAV---------SVEVKDLVRRIKAR-- 184 query 170 ALIARV--DWVSLGGGIHFTGDDYP-----VDAFSARLRAFSDRYGVQ-IYLEPGEASIT 221 ::::: :::::::::: ::::::::: d1ujpa_ 185 ------TALPVAV------------GFGVSGKATAAQAAV--------ADGVVVGSAL-- 216 query 222 KSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAG 281 d1ujpa_ 217 ------------------------------------------------------------ 217 query 282 DVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYA 341 d1ujpa_ 217 ------------------------------------------------------------ 217 query 342 DYEQSLS--------------------------- 348 d1ujpa_ 217 -------VRALEEGRSLAPLLQEIRQGLQRLPLP 243 TMalign alignment (TM-score: 0.36 Raw score:126.07) query 1 ------------------------------------------------------------ 1 d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAGFPSREGFLQAVEEVLPYADLLEIGLPYSDGPVIQR 60 query 1 ----------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKC-FAT---WSV-F 45 :::::::::::::::::::::::::: ::: ::: : d1ujpa_ 61 ASELALRKGM------------SVQGALELVREVRALTEKPLFLMTYLNPVLAWGPERFF 108 query 46 DLMRDY-MDGTTSS-SLF-EVRLGRERFG---KETHAYSVA-YGDNEIDEVVSHA-DKII 97 :::::: ::::::: ::: :::::::::: ::::::::: ::::::::::::: :::: d1ujpa_ 109 GLFKQAGATGVILPDLPPDEDPGLVRLAQEIGLETVFLLAPTSTDARIATVVRHATGFVY 168 query 98 FN---SISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHN-NCENKD 153 :: :::::::::::: ::::::::::: ::::::::: : :::::::: :::: : d1ujpa_ 169 AVSVEVKDLVRRIKART-ALPVAVGFGVS--GKATAAQAA--V--ADGVVVGSALVRA-L 220 query 154 FGLFDRMLGEIEERFGALIAR----VDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGV 209 ::: ::::::::: ::::::: d1ujpa_ 221 EEG-RSLAPLLQE-IRQGLQRLPLP----------------------------------- 243 query 210 QIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSH 269 d1ujpa_ 244 ------------------------------------------------------------ 244 query 270 SYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELD 329 d1ujpa_ 244 ------------------------------------------------------------ 244 query 330 GSVRTVREFTYADYEQSLS 348 d1ujpa_ 244 ------------------- 244 HHsearch alignment (Probability: 0.04 E-value:0.64) query 19 ERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFE----VRLGRERFGKET 74 :::::::::::::::::::::::::::::::::::::::::::: :::::::::::: d1ujpa_ 130 PGLVRLAQEIGLETVFLLAPTSTDARIATVVRHATGFVYAVSVEVKDLVRRIKARTALPV 189 query 75 HAYSVAYGDNEIDEVVSHADKII 97 ::::::::::::::::::::::: d1ujpa_ 190 AVGFGVSGKATAAQAAVADGVVV 212
Intermediate <-- 0.706 --> HitDALI alignment (Z-score: 4.1 Raw score:439.50) d1ujpa_ 1 mttleafakarsegRAALIPYLTA---------------------------------gfp 27 :::::::::: d1qv9a_ 1 --------------TVAKAIFIKCgnlgtsmmmdmllderadredvefrvvgtsvkmdpe 46 d1ujpa_ 28 SREGFLQAVEEVL--PYADLLEIGLPysdgpviqraselalrkgmsVQGALELVREVRAl 85 ::::::::::::: ::::::::::: ::::::::::::: d1qv9a_ 47 CVEAAVEMALDIAedFEPDFIVYGGP-----------------npaAPGPSKAREMLAD- 88 d1ujpa_ 86 TEKPLFLMTYLNPVlawgpeRFFGLFKQAGAtGVILPDLppdedpglvrlaqeigletvf 145 :::::::::::::: ::::::::::: ::::::: d1qv9a_ 89 SEYPAVIIGDAPGL------KVKDEMEEQGL-GYILVKP--damlgarrefldpvemaiy 139 d1ujpa_ 146 llaptstdariatvvrhaTGFVY------------------------------------- 168 ::::: d1qv9a_ 140 nadlmkvlaatgvfrvvqEAFDEliekakedeisendlpklvidrntllereefenpyam 199 d1ujpa_ 169 ------------------------------------------------------------ 169 d1qv9a_ 200 vkamaaleiaenvadvsvegcfveqdkeryvpivasahemmrkaaeladeareleksnda 259 d1ujpa_ 169 avsvEVKDLVRrikartalpvavgfgvsgkataaqaavadgvvvgsalvraleegrslap 228 ::::::: d1qv9a_ 260 vlrtPHAPDGK------------------------------------------------- 270 d1ujpa_ 229 llqeirqglqrlplp 243 d1qv9a_ 271 ---vlskrkfmedpe 282 FAST alignment (Normalized score: 2.81 Raw score:734.40) d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAGF---------------------------------- 26 :::::::: d1qv9a_ 1 --------------TVAKAIFI----KCGNLGTSMMMDMLLDERADREDVEFRVVGTSVK 42 d1ujpa_ 27 PSREGFLQAVEEVLP-----YADLLEIGLPYSDGPVIQRASELALRKGMS-----VQGAL 76 ::::::::::::::: :::::::: ::::: d1qv9a_ 43 MDPECVEAAVEMALDIAEDFEPDFIVYG----------------------GPNPAAPGPS 80 d1ujpa_ 77 ELVREVRALTEKPLFLMTYLNPVLAWGPE--RFFGLFKQAGATGVILPDLPPDEDPGLVR 134 :::::::: :::::::::::: :::::::::: :::::: d1qv9a_ 81 KAREMLAD-SEYPAVIIGDAP--------GLKVKDEMEEQG-LGYILV------------ 118 d1ujpa_ 135 LAQEIGLETVFLLAPTS---------------------TDARIATVVRHATGFVYAVSVE 173 :::::::::: d1qv9a_ 119 -----------------KPDAMLGARREFLDPVEMAIYNADLMKVLAA------------ 149 d1ujpa_ 174 VKDLVRRIKARTALPVAVGFGVSGKATAAQAAVADGVVVGSALVRALEEGRSLAPLLQEI 233 d1qv9a_ 150 ------------------------------------------------------------ 150 d1ujpa_ 234 RQGLQRLPLP-------------------------------------------------- 243 d1qv9a_ 150 ----------TGVFRVVQEAFDELIEKAKEDEISENDLPKLVIDRNTLLEREEFENPYAM 199 d1ujpa_ 244 ------------------------------------------------------------ 244 d1qv9a_ 200 VKAMAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEMMRKAAELADEARELEKSNDA 259 d1ujpa_ 244 ----------------------- 244 d1qv9a_ 260 VLRTPHAPDGKVLSKRKFMEDPE 282 TMalign alignment (TM-score: 0.35 Raw score:85.42) d1ujpa_ 1 MTTLEAFAKAR------------------------SEGRAALIPYLT---AGFPSREGFL 33 :::: ::::::::::: :::::::::: d1qv9a_ 1 -------TVAKAIFIKCGNLGTSMMMDMLLDERAD-REDVEFRVVGTSVKMDPECVEAAV 52 d1ujpa_ 34 QAVEEVL-PY-ADLLEIGLPYSDGPVIQRASELALRKGMSVQGALELVREVRALTEKPLF 91 ::::::: :: :::::::::: ::::::::::::::::::: :: d1qv9a_ 53 EMALDIAEDFEPDFIVYGGPN-----------------PAAPGPSKAREMLADSEYP-AV 94 d1ujpa_ 92 LMTYLNPVLAWGPERFFGLFKQAGATGVILPDLP--------------------PDEDPG 131 ::::: :: : :::::::::::::::::::: d1qv9a_ 95 IIGDA-PG----L-KVKDEMEEQGLGYILVKPDAMLGARREFLDPVEMAIYNAD------ 142 d1ujpa_ 132 LVRLAQEIGLETVFLLAPTSTDARIATVVRHATGFVY----------------------- 168 ::::::: :: ::::::::::: d1qv9a_ 143 --------------LMKVLAA--TG-VFRVVQEAFDELIEKAKEDEISENDLPKLVIDRN 185 d1ujpa_ 169 ------------------------------------------------------------ 169 d1qv9a_ 186 TLLEREEFENPYAMVKAMAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEMMRKAAE 245 d1ujpa_ 169 ---------------AVSVEVKDLVRRIKARTALPVAVGFGVSGKATAAQAAVADG---- 209 :::: : ::::: d1qv9a_ 246 LADEARELEKSNDAV----------LRTP------H---------------APDGKVLSK 274 d1ujpa_ 210 ---VVVGSALVRALEEGRSLAPLLQEIRQGLQRLPL---P 243 :: d1qv9a_ 275 RKF-------------------------------MEDPE- 282 HHsearch alignment (Probability: 0.12 E-value:0.07) d1ujpa_ 19 IPYLTAGFPSREGFLQAVEEVLPYADLLEIGL-PYSDGPVIQRASELALRKGMSVQGALE 77 :::::::: :::::::::::::::::::::: :::::::::::::::: :::::: d1qv9a_ 5 AIFIKCGN--LGTSMMMDMLLDERADREDVEFRVVGTSVKMDPECVEAA-----VEMALD 57 d1ujpa_ 78 LVREVRALTEKPLFLMTYLNPVLAWGPERFFGLFKQAGATGVILPDLPPDEDPGLVRLAQ 137 ::::: :::::::::::::: ::::::::::::::::::::::::::: :::::: d1qv9a_ 58 IAEDF----EPDFIVYGGPNPAA-PGPSKAREMLADSEYPAVIIGDAPGLK---VKDEME 109 d1ujpa_ 138 EIGLETVFLLAPTS-TDAR--------------IATVVRHATGFVYAVSVEVKDLVRRIK 182 :::::::::::::: :::: :::::: :::::::::::::::::::: d1qv9a_ 110 EQGLGYILVKPDAMLGARREFLDPVEMAIYNADLMKVLA-ATGVFRVVQEAFDELIEKAK 168 d1ujpa_ 183 ART----ALPVAV 191 ::: :::::: d1qv9a_ 169 EDEISENDLPKLV 181