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 | d1twia1 | Diaminopimelate decarboxylase LysA | Alanine racemase C-terminal domain-like | Domain of alpha and beta subunits of F1 ATP synthase-like | All β |
| Hit | d1xe1a_ | Hypothetical protein PF0907 | Translation proteins | Reductase/isomerase/elongation factor common domain | All β |
Query <-- 1.176 --> IntermediateDALI alignment (Z-score: 15.7 Raw score:1022.10) query 1 --------------------------MIETPYYLIdkakltrnmeriahvreksgakall 34 ::::::::: d1twia1 1 mlgndtveikdgrffidgydaielaeKFGTPLYVM------------------------- 35 query 35 alkcfatwsvfdlmrdymdgttssslfevrlgrerfgkethaysvaygdneidevvshad 94 d1twia1 36 ------------------------------------------------------------ 36 query 95 kiifnsisqlerfadkaagiarglrlnpqrlgewdvpkvervmdringfmihnncenkdf 154 d1twia1 36 ------------------------------------------------------------ 36 query 155 glfdrmlgeieerfgaliarvdwvslgggihftgddypvdafsarlrafsdrygvqiyle 214 d1twia1 36 ------------------------------------------------------------ 36 query 215 pgeasitksTTLEVTVLDTLYN--KNLAIVDSSIeAHMLDLLIYRETAKVL---pneGSH 269 ::::::::::::: :::::::::: :::::::::::::::: ::: d1twia1 36 ---------GYLLGKVHHIKETpvTKWVMIDAGM-NDMMRPAMYEAYHHIInckvknEKE 85 query 270 SYMICGKSCLAGDVFGE-FRFAeELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIREL 328 ::::::::::::::::: :::: ::::::::::::::::::::::::::::::::::::: d1twia1 86 VVSIAGGLCESSDVFGRdRELD-KVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSK 144 query 329 DgSVRTVRE-FTYADYeQSLS------- 348 : ::::::: :::::: :::: d1twia1 145 K-GVFLIRErETYADL-IAKDivpphll 170 FAST alignment (Normalized score: 8.50 Raw score:2067.00) query 1 --------------------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALL 34 ::::::: d1twia1 1 MLGNDTVEIKDGRFFIDGYDAIELAEKFGTPLY--------------------------- 33 query 35 ALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHAD 94 d1twia1 34 ------------------------------------------------------------ 34 query 95 KIIFNSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDF 154 d1twia1 34 ------------------------------------------------------------ 34 query 155 GLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLE 214 d1twia1 34 ------------------------------------------------------------ 34 query 215 PGEASITKS--TTLEVTVLDTLY---NKNLAIVDSSIEAHMLDLLIYRETAKVLPNEG-- 267 ::::::::::: :::::::::: ::::::::::::::: d1twia1 34 ---------VMGYLLGKVHHIK-ETPVTKWVMIDAG-MNDMMRPAMYEAYHH------II 76 query 268 -------SHSYMICGKSCLAGDVF-GEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVK 319 ::::::::::::::::: ::::: ::::::::::::::::::::::::::::: d1twia1 77 NCKVKNEKEVVSIAGGLCESSDVFGRDREL-DKVEVGDVLAIFDVGAYGISMANNYNARG 135 query 320 MPAIAIRELDGSVRTV-REFTYADYEQSLS------- 348 ::::::::: :::::: :::::::::::: d1twia1 136 RPRMVLTSK-KGVFLIRERETYADLIAKD-IVPPHLL 170 TMalign alignment (TM-score: 0.35 Raw score:122.00) query 1 --------------------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALL 34 ::::::::: d1twia1 1 MLGNDTVEIKDGRFFIDGYDAIELAEKFGTPLYVM------------------------- 35 query 35 ALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHAD 94 d1twia1 36 ------------------------------------------------------------ 36 query 95 KIIFNSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDF 154 d1twia1 36 ------------------------------------------------------------ 36 query 155 GLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLE 214 d1twia1 36 ------------------------------------------------------------ 36 query 215 PGEASITKSTTLEVTVLDTLYN--KNLAIVDSSIEAHMLDLLIYRETAKVLP--NE--GS 268 ::::::::::::: :::::::::: ::::::::::::::::: : :: d1twia1 36 ---------GYLLGKVHHIKETPVTKWVMIDAGM-NDMMRPAMYEAYHHIINCK-VKNEK 84 query 269 HSYMICGKSCLAGDVFGE-FRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRE 327 :::::::::::::::::: ::::: ::::::::::::::::::::::::::::::::::: d1twia1 85 EVVSIAGGLCESSDVFGRDRELDK-VEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTS 143 query 328 LDGSVRTVREF-TYADYEQSLS------ 348 :: :::::::: :::::::::: d1twia1 144 KK-GVFLIRERETYADLIAKDIVPPHLL 170 HHsearch alignment (Probability: 1.00 E-value:0.00) query 208 GVQIYLEPGEASITKSTTLEVTVLDTLY--NKNLAIVDSSIEAHMLDLLIYRETAKVLP- 264 :::::::::::::: ::::::::::::: :::::::::::: :::::::::::::::: d1twia1 21 AIELAEKFGTPLYV-MGYLLGKVHHIKETPVTKWVMIDAGMN-DMMRPAMYEAYHHIINC 78 query 265 --NEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPA 322 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1twia1 79 KVKNEKEVVSIAGGLCESSDVFGRDRELDKVEVGDVLAIFDVGAYGISMANNYNARGRPR 138 query 323 IAIRELDGSVRTVREFTYADYEQS 346 :::::::::::::::::::::::: d1twia1 139 MVLTSKKGVFLIRERETYADLIAK 162
Intermediate <-- 1.011 --> HitDALI alignment (Z-score: 2.5 Raw score:224.00) d1twia1 1 --MLGNdtveikdgrffidgydaielaekfgtplyvmgYLLGKVHHIKETPVTKWVMIDA 58 :::: :::::::::::::::::::::: d1xe1a_ 1 ieILSK------------------------------kpAGKVVVEEVVNIMGKDVIIGTV 30 d1twia1 59 gmndmmrpamyeAYHHIINckvknekevvsiaggLCESSD---------vfgRDRELDKV 109 ::::::: :::::: :::::::: d1xe1a_ 31 ------esgmigVGFKVKG----psgiggivrieRNREKVefaiagdrigisIEGKIGKV 80 d1twia1 110 EVGDVLAIFDvgaygismannynargrprmvltskkgvflireretyadliakdivpphl 169 :::::::::: d1xe1a_ 81 KKGDVLEIYQ-------------------------------------------------- 90 d1twia1 170 l 170 d1xe1a_ 91 t 91 FAST alignment (Normalized score: 2.80 Raw score:348.70) d1twia1 1 MLGNDTVEIKDGRFFIDGYDAIELAEKFGTPLYVMG--------YLLGKVHHIKETPVTK 52 :::::::::::::::: d1xe1a_ 1 ------------------------------------IEILSKKPAGKVVVEEVVNIMGKD 24 d1twia1 53 WVMIDAGMNDMMRPAMYE--------AYHHIINCKVKNEKEVVS--------IAGGLCES 96 :::: ::::::: ::::::: d1xe1a_ 25 VIIG--------------TVESGMIGVGFKVKG-----------PSGIGGIVRIERNRE- 58 d1twia1 97 SDVFG--------------RDRELDKVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLT 142 :::::::::::::::: d1xe1a_ 59 -----KVEFAIAGDRIGISIEGKIGKVKKGDVLEI------------------------- 88 d1twia1 143 SKKGVFLIRERETYADLIAKDIVPPHLL--- 170 d1xe1a_ 89 ----------------------------YQT 91 TMalign alignment (TM-score: 0.34 Raw score:57.94) d1twia1 1 --MLGNDTVEIKDGRFFIDGYDAIELAEKFGTPLYVMGYLLGKVHHIKETPVTKWVMIDA 58 :::: : ::::::::::::::::::::::: d1xe1a_ 1 IEILSK--K----------------------------PAGKVVVEEVVNIMGKDVIIGTV 30 d1twia1 59 G-MNDMMRPAMYEAYHHIINCKVKNEK-EVVSIAGGL-CESSD--------VFGRDRELD 107 : ::::: :::::: :: : :::::::: ::::: ::::::::: d1xe1a_ 31 ES--GMIGV-----GFKVKG--PS--GI-GGIVRIERNREKVEFAIAGDRIGISIEGKIG 78 d1twia1 108 KVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSKKGVFLIRERETYADLIAKDIVPP 167 ::::::::::::: d1xe1a_ 79 KVKKGDVLEIYQT----------------------------------------------- 91 d1twia1 168 HLL 170 d1xe1a_ 92 --- 92 HHsearch alignment (Probability: 0.01 E-value:0.21) d1twia1 98 DVFGRDRELD--KVEVGDVLAIFD 119 :::::::::: :::::::::::: d1xe1a_ 67 DRIGISIEGKIGKVKKGDVLEIYQ 90