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 | d1twia2 | Diaminopimelate decarboxylase LysA | PLP-binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1ct5a_ | (Hypothetical( protein ybl036c | PLP-binding barrel | TIM beta/alpha-barrel | α/β |
Query <-- 1.000 --> IntermediateDALI alignment (Z-score: 20.6 Raw score:1900.40) query 1 mietpyyliDKAKLTRNMERIAHVREKSG------AKALLALKCFATWSVFDLMRDYMDG 54 :::::::::::::::::::: ::::::::::::::::::::::::: d1twia2 1 ---------SEEQIKINYNRYIEAFKRWEeetgkeFIVAYAYKANANLAITRLLAKLGCG 51 query 55 TTSSSLFEVRLGRERFGK--ETHAYSVAYGDNEIDEVVSH-ADKIIFNSISQLERFADKA 111 :::::::::::::::::: :::::::::::::::::::: ::::::::::::::::::: d1twia2 52 ADVVSGGELYIAKLSNVPskKIVFNGNCKTKEEIIMGIEAnIRAFNVDSISELILINETA 111 query 112 ----AGIARGLRLNPQ----------------RLGEW----DVPKVERVMD-----RING 142 :::::::::::: ::::: :::::::::: :::: d1twia2 112 kelgETANVAFRINPNvnpkthpkistglkknKFGLDvesgIAMKAIKMALemeyvNVVG 171 query 143 FMIHNNCENKDFGLFDRMLGEIEERFGAL---iARVDWVSLGGGIH----ftgDDYPVDA 195 ::::::::::::::::::::::::::::: ::::::::::::: ::::::: d1twia2 172 VHCHIGSQLTDISPFIEETRKVMDFVVELkeegIEIEDVNLGGGLGipyykdkQIPTQKD 231 query 196 FSARLRAFSDR-----YGVQIYLEPGEASITKSttlevtvldtlynknlaivdssieahm 250 ::::::::::: ::::::::::::::::: d1twia2 232 LADAIINTMLKykdkvEMPNLILEPGRSLVATA--------------------------- 264 query 251 ldlliyretakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmv 310 d1twia2 265 ------------------------------------------------------------ 265 query 311 kknwfngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1twia2 265 -------------------------------------- 265 FAST alignment (Normalized score: 11.66 Raw score:3534.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS-------GAKALLALKCFATWSVFDLMRDYM- 52 :::::::::::::::::: :::::::::::::::::::::: d1twia2 1 ---------SEEQIKINYNRYIEAFKR-WEEETGKEFIVAYAYKANANLAITRLLAK--L 48 query 53 -DGTTSSSLFEVRLGRERFGK------ETHAYSVAYGDNEIDEVVS-HADKIIFNSISQL 104 :::::::::::::::: ::::::::::::::::::: ::::::::::::: d1twia2 49 GCGADVVSGGELYIAKL----SNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISEL 104 query 105 ERFADKAA-----GIARGLRLNP-----------------QRLGEWDV----PKVERVMD 138 ::::::: ::::::::: ::::: :::::::: d1twia2 105 ILINETA-KELGETANVAFRIN-PNVNPKTHPKISTGLKKNKFGL---DVESGIAMKAIK 159 query 139 --------RINGFMIHNNCENKDFGLFDRMLGEIEERFGALIA-------RVDWVSLGGG 183 ::::::::::::::::::::::::::::::: :::::::::: d1twia2 160 MALEMEYVNVVGVHCHIGSQLTDISPFIEETRKVMDFVV----ELKEEGIEIEDVNLGGG 215 query 184 IHFTGDDY-----------PVDAFSARLRAFSDRY------GVQIYLEPGEASITKSTTL 226 : ::::::::::::::: :::::::::::::: d1twia2 216 L-------GIPYYKDKQIPTQKDLADAIINTMLK-YKDKVEMPNLILEPGRSLVA----- 262 query 227 EVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGE 286 d1twia2 263 ------------------------------------------------------------ 263 query 287 FRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQS 346 d1twia2 263 ------------------------------------------------------------ 263 query 347 LS-- 348 d1twia2 263 --TA 264 TMalign alignment (TM-score: 0.55 Raw score:190.21) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSG------AKALLALKCFATWSVFDLMRDYMDG 54 :::::::::::::::::::: ::::::::::::::::::::::::: d1twia2 1 ---------SEEQIKINYNRYIEAFKRWEEETGKEFIVAYAYKANANLAITRLLAKLGCG 51 query 55 TTSSSLFEVRLGRERFGK--ETHAYSVAYGDNEIDEVVSH-ADKIIFNSISQLERFADKA 111 :::::::::::::::::: :::::::::::::::::::: ::::::::::::::::::: d1twia2 52 ADVVSGGELYIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISELILINETA 111 query 112 ----AGIARGLRLNP-------------Q---RLGEW--DV--PKVERVMD----R-ING 142 ::::::::::: : ::::: :: :::::::: : ::: d1twia2 112 KELGETANVAFRINPNVNPKTHPKISTGLKKNKFGLDVESGIAMKAIKMALEMEYVNVVG 171 query 143 FMIHNNCENKDFGLFDRMLGEIEERFGALI---ARVDWVSLGGGIHFTG----DDYPVDA 195 :::::::::::::::::::::::::::::: :::::::::::::::: ::::::: d1twia2 172 VHCHIGSQLTDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGGLGIPYYKDKQIPTQKD 231 query 196 FSARLRA-FS-DR--Y-GVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHM 250 ::::::: :: :: : :::::::::::::::: d1twia2 232 LADAIINTMLKYKDKVEMPNLILEPGRSLVATA--------------------------- 264 query 251 LDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMV 310 d1twia2 265 ------------------------------------------------------------ 265 query 311 KKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1twia2 265 -------------------------------------- 265 HHsearch alignment (Probability: 1.00 E-value:0.00) query 10 DKAKLTRNMERIAHVREKS------GAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEV 63 ::::::::::::::::::: ::::::::::::::::::::::::::::::::::: d1twia2 1 SEEQIKINYNRYIEAFKRWEEETGKEFIVAYAYKANANLAITRLLAKLGCGADVVSGGEL 60 query 64 RLGRERFGK-ETHAYSV-AYGDNEIDEVVSHAD-KIIFNSISQLERFADKA----AGIAR 116 ::::::::: ::::::: ::::::::::::::: ::::::::::::::::: ::::: d1twia2 61 YIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISELILINETAKELGETANV 120 query 117 GLRLNP----------------QRLGEWDV-----PKVERVMD----RINGFMIHNNCEN 151 :::::: :::::::: :::::::: ::::::::::::: d1twia2 121 AFRINPNVNPKTHPKISTGLKKNKFGLDVESGIAMKAIKMALEMEYVNVVGVHCHIGSQL 180 query 152 KDFGLFDRMLGEIEERFGAL---IARVDWVSLGGGIHFTGDDY----PVDAFSARLRAFS 204 :::::::::::::::::::: :::::::::::::::::::: ::::::::::::: d1twia2 181 TDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGGLGIPYYKDKQIPTQKDLADAIINTM 240 query 205 -----DRYGVQIYLEPGEASITKS 223 ::::::::::::::::::: d1twia2 241 LKYKDKVEMPNLILEPGRSLVATA 264
Intermediate <-- 0.985 --> HitDALI alignment (Z-score: 18.7 Raw score:1753.40) d1twia2 1 --------SEEQIKINYNRYIEAFKRWEEETgkEFIVAYAYKaNANLAITRLLAKLGC-G 51 ::::::::::::::::::::::: ::::::::: ::::::::::::::: : d1ct5a_ 1 tgitydedRKTQLIAQYESVREVVNAEAKNV--KILLLVVSK-LKPASDIQILYDHGVrE 57 d1twia2 52 ADVVSGGELYIAK-LSNVPSkKIVFNGNCKTKEeIIMGIEAN-IRAFN-VDSISELILIN 108 ::::::::::::: :::::: :::::::::::: :::::::: ::::: ::::::::::: d1ct5a_ 58 FGENYVQELIEKAkLLPDDI-KWHFIGGLQTNK-CKDLAKVPnLYSVEtIDSLKKAKKLN 115 d1twia2 109 ETAKELGE---TANVAFRINPnvnpkthpkISTGlkkNKFGLDvESGIAMKAIKMALE-- 163 :::::::: :::::::::: :::: :::::: :::::::::::::: d1ct5a_ 116 ESRAKFQPdcnPILCNVQINT---------SHED---QKSGLN-NEAEIFEVIDFFLSee 162 d1twia2 164 MEYVNVVGVHCHIGSqltdispfIEETRKVMDFVVELKEE-GIEIeDVNLGGGLgipyyk 222 ::::::::::::::: ::::::::::::::::: :::: :::::::: d1ct5a_ 163 CKYIKLNGLMTIGSW--------NRDFATLVEWKKKIDAKfGTSL-KLSMGMSA------ 207 d1twia2 223 dkqiptqkdLADAIINTMlkykdkvempnLILEPGRSLVAta 264 ::::::::: ::::::::::: d1ct5a_ 208 ---------DFREAIRQG----------tAEVRIGTDIFG-- 228 FAST alignment (Normalized score: 12.98 Raw score:3184.00) d1twia2 1 --------SEEQIKINYNRYIEAFKRWEEETGKEFIVAYAYKANANLAITRLLAKLG-CG 51 :::::::::::::::::::::: ::::::::::: ::::::::::::: :: d1ct5a_ 1 TGITYDEDRKTQLIAQYESVREVVNAEAKN--VKILLLVVSKL-KPASDIQILYDHGVRE 57 d1twia2 52 ADVVSGGELYIAKLSNVPSK-KIVFNGNCKTKEEIIMGIEA-NIRAF-NVDSISELILIN 108 :::::::::::::: ::::: :::::: ::::::::::::: ::::: :::::::::::: d1ct5a_ 58 FGENYVQELIEKAK-LLPDDIKWHFIG-GLQTNKCKDLAKVPNLYSVETIDSLKKAKKLN 115 d1twia2 109 ETAKEL----GETANVAFRINPNVNPKTHPKISTG--LKKNKFGLDVES----GIAMKAI 158 ::::: ::::::::::: ::::::: ::::::: d1ct5a_ 116 ESRAK-FQPDCNPILCNVQIN--------------TSHEDQKSG-----LNNEAEIFEVI 155 d1twia2 159 KMAL---EMEYVNVVGVHCHIGSQLTDISP-FIEETRKVMDFVVELK-EEGIEIEDVNLG 213 ::: :::::::::::::: :::::::::::::::: :::::: d1ct5a_ 156 DFF-LSEECKYIKLNGLMTIG---------SWNRDFATLVEWKKKIDAKFGTSL------ 199 d1twia2 214 GGLGIPYYKDKQIPTQKD--------LADAIINTMLKYKDKVEMPN---LILEPGRSLVA 262 ::::::: :::::::::: d1ct5a_ 200 ------------------KLSMGMSADFREAIR-------------QGTAEVRIGTDIF- 227 d1twia2 263 TA- 264 d1ct5a_ 228 --G 228 TMalign alignment (TM-score: 0.67 Raw score:178.19) d1twia2 1 --------SEEQIKINYNRYIEAFKRWEEETGKEFIVAYAYKANANLAITRLLAKLGC-G 51 ::::::::::::::::::::::: ::::::::::: ::::::::::::: : d1ct5a_ 1 TGITYDEDRKTQLIAQYESVREVVNAEAKNV--KILLLVVSKLK-PASDIQILYDHGVRE 57 d1twia2 52 ADVV-SGGELYIAKLSNVPSKKIVFN-GNCK-TKEEIIMGIEANIRAFN-VDSISELILI 107 :::: ::::::::::::::: ::::: :::: :::::::: :: ::::: :::::::::: d1ct5a_ 58 FGENYVQELIEKAKLLPDDI-KWHFIGGLQTNKCKDLAKV-PN-LYSVETIDSLKKAKKL 114 d1twia2 108 NETAKEL-GE--TANVAFRINPNVNPKTHPKISTGLKKNKFGLDVESGIAMKAIKMALE- 163 ::::::: :: :::::::::: : :: ::: :::: :::::::::::::: d1ct5a_ 115 NESRAKFQPDCNPILCNVQINT-S--------HE--DQK-SGLN-NEAEIFEVIDFFLSE 161 d1twia2 164 MEY-VNVVGVHCHIGSQLTDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGGLGIPYYK 222 ::: ::::::::::: : :::::::::::::::::::::::::::: :: d1ct5a_ 162 ECKYIKLNGLMTIGS-------W-NRDFATLVEWKKKIDAKFGTSLKLSMGM-SA----- 207 d1twia2 223 DKQIPTQKDLADAIINTMLKYKDKVEMPNLILEPGRSLVATA 264 ::: :::::: : ::::::::::: d1ct5a_ 208 --------DFR-EAIRQG---------T-AEVRIGTDIFG-- 228 HHsearch alignment (Probability: 0.99 E-value:0.00) d1twia2 3 EQIKINYNRYIEAFKRWEEETGKEFIVAYAYKANANLAITRLLAKLGCGADVVSGGELYI 62 :::::::::::::::::: :::::::::::::::::::::::::::::::::::::::: d1ct5a_ 11 TQLIAQYESVREVVNAEA--KNVKILLLVVSKLKPASDIQILYDHGVREFGENYVQELIE 68 d1twia2 63 AKLSNVPSKKIVFNGNCKTKEEIIMGIEA-NIR-AFNVDSISELILINETAKELGETAN- 119 :::::::::::::::::: :::::::::: ::: ::::::::::::::::::::::::: d1ct5a_ 69 KAKLLPDDIKWHFIGGLQ-TNKCKDLAKVPNLYSVETIDSLKKAKKLNESRAKFQPDCNP 127 d1twia2 120 --VAFRINPNVNPKTHPKISTGLKKNKFGLDVE-SGIAMKAIKMALEMEYVNVVGVHCHI 176 ::::::: :::::::::::: :::::::::::::::::::::: ::: d1ct5a_ 128 ILCNVQINT------------SHEDQKSGLNNEAEIFEVIDFFLSEECKYIKLNGL-MTI 174 d1twia2 177 GSQLTDISPFIEETRKVMDFVVELKEEGIEIEDVNLGG 214 ::::::: :::::::::::::::::::::::: d1ct5a_ 175 GSWNRDF-------ATLVEWKKKIDAKFGTSLKLSMGM 205