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 | d7odca2 | Eukaryotic ornithine decarboxylase | 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 <-- 1.000 --> HitDALI alignment (Z-score: 27.0 Raw score:2452.40) d1twia2 1 SEEQIKINYNRYIEAFKrweeetgkEFIVAYAYKANANLAITRLLAKLGCGADVVSGGEL 60 ::::::::::::::::: ::::::::::::::::::::::::::::::::::: d7odca2 1 DLGDILKKHLRWLKALP--------RVTPFYAVKCNDSRAIVSTLAAIGTGFDCASKTEI 52 d1twia2 61 YIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISELILINETAkelgETANV 120 ::::::::::::::::::::::::::::::::::::::::::::::::::: ::::: d7odca2 53 QLVQGLGVPAERVIYANPCKQVSQIKYAASNGVQMMTFDSEIELMKVARAH----PKAKL 108 d1twia2 121 AFRINPnvnpkthpkistglkknKFGLDVesGIAMKAIKMALEMEyVNVVGVHCHIGSQL 180 :::::: :::::: :::::::::::::: :::::::::::::: d7odca2 109 VLRIAT-----------------KFGATL--KTSRLLLERAKELN-IDVIGVSFHVGSGC 148 d1twia2 181 TDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGGLGIPYYkdkQIPTQKDLADAIINTM 240 ::::::::::::::::::::::::::::::::::::::::: :::::::::::::::: d7odca2 149 TDPDTFVQAVSDARCVFDMATEVGFSMHLLDIGGGFPGSED---TKLKFEEITSVINPAL 205 d1twia2 241 LK-YKDKvEMPNLILEPGRSLVATA 264 :: :::: ::::::::::::::::: d7odca2 206 DKyFPSD-SGVRIIAEPGRYYVASA 229 FAST alignment (Normalized score: 22.03 Raw score:5416.00) d1twia2 1 SEEQIKINYNRYIEAFKRWEEETGK-EFIVAYAYKANANLAITRLLAKLGCGADVVSGGE 59 :::::::::::::::: :::::::::::::::::::::::::::::::::: d7odca2 1 DLGDILKKHLRWLKAL---------PRVTPFYAVKCNDSRAIVSTLAAIGTGFDCASKTE 51 d1twia2 60 LYIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISELILINETAKELG-ETA 118 ::::::::::::::::::::::::::::::::::::::::::::::::::: ::: d7odca2 52 IQLVQGLGVPAERVIYANPCKQVSQIKYAASNGVQMMTFDSEIELMKVARA-----HPKA 106 d1twia2 119 NVAFRINPNVNPKTHPKISTGLKK-NKFGLDVESGIAMKAIKMALEMEYVNVVGVHCHIG 177 :::::: ::::::: ::::::::::::: ::::::::::: d7odca2 107 KLVLRI------------------ATKFGATL--KTSRLLLERAKEL-NIDVIGVSFHV- 144 d1twia2 178 -SQLTDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGGLGIPYYKDKQ-----IPTQKD 231 :::::::::::::::::::::::::::::::::::::::: :::::: d7odca2 145 GSGCTDPDTFVQAVSDARCVFDMATEVGFSMHLLDIGGGFP--------GSEDTKLKFEE 196 d1twia2 232 LADAIINTMLK--YKDKVEMPNLILEPGRSLVATA- 264 ::::::::::: ::: :::::::::::::::: d7odca2 197 ITSVINPALDKYFPSD--SGVRIIAEPGRYYVAS-A 229 TMalign alignment (TM-score: 0.79 Raw score:207.74) d1twia2 1 SEEQIKINYNRYIEAFKRWEEETGKEFIVAYAYKANANLAITRLLAKLGCGADVVSGGEL 60 ::::::::::::::::: : :::::::::::::::::::::::::::::::::: d7odca2 1 DLGDILKKHLRWLKALP-R-------VTPFYAVKCNDSRAIVSTLAAIGTGFDCASKTEI 52 d1twia2 61 YIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISELILINETAKELGETANV 120 :::::::::::::::::::::::::::::::::::::::::::::::::::: :::: d7odca2 53 QLVQGLGVPAERVIYANPCKQVSQIKYAASNGVQMMTFDSEIELMKVARAHP----KAKL 108 d1twia2 121 AFRINPNVNPKTHPKISTGLKKNKFGLDVESGIAMKAIKMALEMEYVNVVGVHCHIGSQL 180 :::::: ::::::: : :::::::::::: :::::::::::::: d7odca2 109 VLRIAT-----------------KFGATLK-T-SRLLLERAKELN-IDVIGVSFHVGSGC 148 d1twia2 181 TDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGGLGIPYYKDKQIPTQKDLADAIINTM 240 :::::::::::::::::::::::::::::::::::::::::: : ::: ::::::::::: d7odca2 149 TDPDTFVQAVSDARCVFDMATEVGFSMHLLDIGGGFPGSEDT-K-LKF-EEITSVINPAL 205 d1twia2 241 LKYKD-KVEMPNLILEPGRSLVATA 264 ::::: :::::::::::::::::: d7odca2 206 DKYFPS-DSGVRIIAEPGRYYVASA 229 HHsearch alignment (Probability: 1.00 E-value:0.00) d1twia2 3 EQIKINYNRYIEAFKRWEEETGKEFIVAYAYKANANLAITRLLAKLGCGADVVSGGELYI 62 :::::::::::::: :::::::::::::::::::::::::::::::::::::: d7odca2 3 GDILKKHLRWLKAL--------PRVTPFYAVKCNDSRAIVSTLAAIGTGFDCASKTEIQL 54 d1twia2 63 AKLSNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISELILINETAKELGETANVAF 122 ::::::::::::::::::::::::::::::::::::::::::::::::: ::::::: d7odca2 55 VQGLGVPAERVIYANPCKQVSQIKYAASNGVQMMTFDSEIELMKVARAH----PKAKLVL 110 d1twia2 123 RINPNVNPKTHPKISTGLKKNKFGLDVESGIAMKAIKMALEMEYVNVVGVHCHIGSQLTD 182 ::: ::::::::::: :::::::: :::::::::::::::::: d7odca2 111 RIA-----------------TKFGATLKTSR--LLLERAKE-LNIDVIGVSFHVGSGCTD 150 d1twia2 183 ISPFIEETRKVMDFVVELKEEGIEIEDVNLGGGLGIPYYKDKQIPTQKDLADAIINTMLK 242 ::::::::::::::::::::::::::::::::::::::: :::::::::::::::::: d7odca2 151 PDTFVQAVSDARCVFDMATEVGFSMHLLDIGGGFPGSED---TKLKFEEITSVINPALDK 207 d1twia2 243 YKDKVEMPNLILEPGRSLVATA 264 :::::::::::::::::::::: d7odca2 208 YFPSDSGVRIIAEPGRYYVASA 229