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 | d1q6oa_ | 3-keto-L-gulonate 6-phosphate decarboxylase | Ribulose-phoshate binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d5ruba1 | Ribulose 1,5-bisphosphate carboxylase-oxygenase | RuBisCo, C-terminal domain | TIM beta/alpha-barrel | α/β |
Query <-- 1.541 --> IntermediateDALI alignment (Z-score: 13.1 Raw score:1148.30) query 1 mietpyylidkakltrnmeriahvreksGAKALLALKC---fATWSVFDLMRDYMDGTTS 57 :::::::::: :::::::::::::::::: d1q6oa_ 1 ----------------------------LPMLQVALDNqtmdSAYETTRLIAEEVDIIEV 32 query 58 S-------SLFEVRLGRERFG-KETHAYS-VAYG-DNEIDEVVS-HADKIIFNS---ISQ 103 : ::::::::::::: ::::::: :::: ::::::::: ::::::::: ::: d1q6oa_ 33 GtilcvgeGVRAVRDLKALYPhKIVLADAkIADAgKILSRMCFEaNADWVTVICcadINT 92 query 104 LERFADKAA--GIARGLRLNPQrlgeWDVPKVERVM-DRINGFMIHNNCE-NKDFgLFDR 159 ::::::::: ::::::::::: :::::::::: ::::::::::::: :::: :::: d1q6oa_ 93 AKGALDVAKefNGDVQIELTGY----WTWEQAQQWRdAGIGQVVYHRSRDaQAAG-VAWG 147 query 160 mlGEIEERFGALIARVDWVSLGGGIHFtgddypvdAFSARLRAFSdrygvQIYLEPGEAS 219 ::::::::::::::::::::::::: :::::::::: :::::::::: d1q6oa_ 148 --EADITAIKRLSDMGFKVTVTGGLAL--------EDLPLFKGIP-----IHVFIAGRSI 192 query 220 -ITKSttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsymicgksc 278 :::: d1q6oa_ 193 rDAAS------------------------------------------------------- 197 query 279 lagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvref 338 d1q6oa_ 198 ------------------------------------------------------pveaar 203 query 339 tyadyeqsls 348 d1q6oa_ 204 qfkrsiaelw 213 FAST alignment (Normalized score: 5.19 Raw score:1413.00) query 1 MIETPYYL----------IDKAKLTRNMERIAHVREKSGAKALLALKCFA----TWSVFD 46 ::::::::::: :::::: ::::: :::: :::::: d1q6oa_ 1 --------LPMLQVALDNQTMDSAYETTR---LIAEEV-DIIEV-GTIL-CVGEGVRAVR 46 query 47 LMRDYM-----DGTTSS-----SLFEVRLGRERF--GKETHAYSVAYGDNEIDEVVSHA- 93 ::::: ::::: :::::::::: ::::: :::::::::::::::: d1q6oa_ 47 DLKAL-YPHKIVLADA-KIADAGKILSRMCFE--ANADWVT-VICCADINTAKGALDV-A 100 query 94 ----DKIIF-----NSISQLERFADKAAGIARGLRLNPQRLGEW---------------D 129 ::::: ::::::::::: ::: :::::: : d1q6oa_ 101 KEFNGDVQIELTGYWTWEQAQQWRD--AGI-GQVVYH-------RSRDAQAAGVAWGEAD 150 query 130 VPKVERVMDRI--NGFMIHNNCENKDFGL---FDRMLGEIEERFGALIARVDWVSLGGGI 184 ::::::::: :::::: ::::: ::::: ::::::: d1q6oa_ 151 ITAIKRLSD--MGFKVTVT----------GGLALEDL----PLFKG--IPIHVFI----- 187 query 185 HFTGDD--------YPVDAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYN 236 ::::::::::::::::: d1q6oa_ 188 ------AGRSIRDAASPVEAARQFKRSIAEL----------------------------- 212 query 237 KNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVG 296 d1q6oa_ 213 ------------------------------------------------------------ 213 query 297 DRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS- 348 d1q6oa_ 213 ----------------------------------------------------W 213 TMalign alignment (TM-score: 0.43 Raw score:149.47) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF---ATWSVFDLMRDYMDGTTS 57 ::::::::::: :::::::::::::::::: d1q6oa_ 1 ----------------------------LPMLQVALDNQTMDSAYETTRLIAEEVDIIEV 32 query 58 -S--S----LFEVRLGRERFG-KETHAYSVAY-G-DNEIDEVVS-HADKIIFN--S-ISQ 103 : : :::::::::::: :::::::::: : ::::::::: :::::::: : ::: d1q6oa_ 33 GTILCVGEGVRAVRDLKALYPHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINT 92 query 104 LERFADKAA--GIARGLRLNPQRLGEWDVPKVERVMD-RINGFMIHNNCE-NK--DFGLF 157 ::::::::: ::::::::: : :::::::::::: :::::::::::: :: ::: d1q6oa_ 93 AKGALDVAKEFNGDVQIELT---G-YWTWEQAQQWRDAGIGQVVYHRSRDAQAAG--VAW 146 query 158 DRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGE 217 : ::::::::::::::::::::::::: : ::::::::: :: :::::: d1q6oa_ 147 -G--EADITAIKRLSDMGFKVTVTGGLAL-----E---DLPLFKGIP----IH-VFIAGR 190 query 218 ASITKST----------------TLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAK 261 ::::::: d1q6oa_ 191 SIRDAASPVEAARQFKRSIAELW------------------------------------- 213 query 262 VLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMP 321 d1q6oa_ 214 ------------------------------------------------------------ 214 query 322 AIAIRELDGSVRTVREFTYADYEQSLS 348 d1q6oa_ 214 --------------------------- 214 HHsearch alignment (Probability: 0.38 E-value:0.02) query 16 RNMERIAHVREKSGAKALLALKCFATWSV-FDLMRDYMDGTTSSS--------LFEVRLG 66 :::::::::: ::::::::::::::::: ::::::::::::::: ::::::: d1q6oa_ 43 RAVRDLKALY--PHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINTAKGALDVA 100 query 67 RERFGKETHAYSVAYGDNEIDEVVSHADKIIF-------------NSISQLERFADKAAG 113 :::::::::::::::::::::::::::::::: :::::::::::: :: d1q6oa_ 101 KEFNGDVQIELTGYWTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRL-SD 159 query 114 IARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGAL 171 :::::::::::::::::::::::::::: ::::::::::::::::::::::::: d1q6oa_ 160 MGFKVTVTGGLALEDLPLFKGIPIHVFI-----AGRSIRDAASPVEAARQFKRSIAEL 212
Intermediate <-- 1.578 --> HitDALI alignment (Z-score: 13.5 Raw score:1354.40) d1q6oa_ 1 --------------------LPMLQVALDN---QTMDSAYETTRLIAEEVDIIEVGTILC 37 :::::::::: ::::::::::::::::::::::::::: d5ruba1 1 gpsvnisalwkvlgrpevdgGLVVGTIIKPklgLRPKPFAEACHAFWLGGDFIKNDEPQG 60 d1q6oa_ 38 V---GEGVRAVRDLKALYP--------HKIVLADAkIADA---GKILSRMCFEAN----- 78 : ::::::::::::::: :::::::: :::: :::::::::::: d5ruba1 61 NqpfAPLRDTIALVADAMRraqdetgeAKLFSANI-TADDpfeIIARGEYVLETFgenas 119 d1q6oa_ 79 aDWVTVICC-ADINTAKGALDVAKefNGDVQIELTGY------------wTWEQAQQWRD 125 :::::::: :::::::::::::: ::::::::::: :::::::::: d5ruba1 120 hVALLVDGYvAGAAAITTARRRFP--DNFLHYHRAGHgavtspqskrgytAFVHCKMARL 177 d1q6oa_ 126 AGIGQVVYHRsrdaqaagvawgEADITAIKRLSD---------------MGFKVTVTgGL 170 :::::::::: :::::::::::: :::::::: :: d5ruba1 178 QGASGIHTGT------------SSDRAIAYMLTQdeaqgpfyrqswggmKACTPIIS-GG 224 d1q6oa_ 171 AL-EDLPLFK---GIPIHVFIAGRS-irdaASPVEAARQFKRSIAELW------------ 213 :: ::::::: :::::::::::: :::::::::::::::::: d5ruba1 225 MNaLRMPGFFenlGNANVILTAGGGafghiDGPVAGARSLRQAWQAWRdgvpvldyareh 284 d1q6oa_ 214 --------------------------- 214 d5ruba1 285 kelarafesfpgdadqiypgwrkalgv 311 FAST alignment (Normalized score: 9.67 Raw score:2490.00) d1q6oa_ 1 --------------------LPMLQVALDN-----QTMDSAYETTRLIAEEVDIIEVGTI 35 :::::::: ::::::::::::::::::::::::: d5ruba1 1 GPSVNISALWKVLGRPEVDGGLVVGTII--KPKLGLRPKPFAEACHAFWLGGDFIKNDEP 58 d1q6oa_ 36 LC--VGEG-VRAVRDLKALYP--------HKIVLADAKIAD---AGKILSRMCFEANA-- 79 :: :::: :::::::::::: ::::::::::: ::::::::::: d5ruba1 59 QGNQPFAPLRDTIALVADAMRRAQDETGEAKLFSANITAD-DPFEIIARGEYVLE---TF 114 d1q6oa_ 80 ------DWVTVI-CCADINTAKGALDVAKEFNGDVQIELTGYW---------------TW 117 :::::: ::::::::::::::: :::::::::: :: d5ruba1 115 GENASHVALLVDGYVAGAAAITTARRRF--PDNFLHYHRA---GHGAVTSPQSKRGYTAF 169 d1q6oa_ 118 EQAQQWRDAGIGQVVYHRSRDAQAAGVAWGE---ADITAIKRLSDM-------------- 160 :::::::::::::::: ::::::::: d5ruba1 170 VHCKMARLQGASGIHT---------------GTSSDRAIAYML---TQDEAQGPFYRQSW 211 d1q6oa_ 161 ----GFKVTVTGGLALEDLPLFKGIP--------IHVFIAGRSI---RDAA-SPVEAARQ 204 ::::::::::::::::: ::::::: :::: :::::::: d5ruba1 212 GGMKACTPIISGGMNALRMPG-----FFENLGNANVILTAG---GGAFGHIDGPVAGARS 263 d1q6oa_ 205 FKRSIAELW----------------------------------------- 213 ::::::: d5ruba1 264 LRQAWQA--WRDGVPVLDYAREHKELARAFESFPGDADQIYPGWRKALGV 311 TMalign alignment (TM-score: 0.73 Raw score:156.22) d1q6oa_ 1 --------------------LPMLQVALDN--QT-MDSAYETTRLIAEEVDIIEVGTILC 37 :::::::::: :: ::::::::::::::::::::::::: d5ruba1 1 GPSVNISALWKVLGRPEVDGGLVVGTIIKPKLGLRPKPFAEACHAFWLGGDFIKNDEPQG 60 d1q6oa_ 38 -V-GEGV-RAVRDLKALYP--------HKIVLADAKIADAGKILSRMCFEAN--A----- 79 : :::: ::::::::::: :::::::: :::::::::::::::: : d5ruba1 61 NQPFAPLRDTIALVADAMRRAQDETGEAKLFSANI-TADDPFEIIARGEYVLETFGENAS 119 d1q6oa_ 80 -DWVTVICC-ADINTAKGALDVAKEFNGDVQIELTGY---W-------T--WEQAQQWRD 125 :::::::: :::::::::::::: ::::::::::: : : ::::::::: d5ruba1 120 HVALLVDGYVAGAAAITTARRRFP--DNFLHYHRAGHGAVTSPQSKRGYTAFVHCKMARL 177 d1q6oa_ 126 AGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSDM---------------GFKVTVTGGL 170 ::::::::: : ::::::::::::: ::::::: :: d5ruba1 178 QGASGIHTG-----------T-SSDRAIAYMLTQDEAQGPFYRQSWGGMKACTPIIS-GG 224 d1q6oa_ 171 AL-EDL-PLFK--GIPIHVFIAGRSIRDAA-SPVEAARQFKRSIAELW------------ 213 :: ::: :::: ::::::::::::::::: ::::::::::::::::: d5ruba1 225 MNALRMPGFFENLGNANVILTAGGGAFGHIDGPVAGARSLRQAWQAWRDGVPVLDYAREH 284 d1q6oa_ 214 --------------------------- 214 d5ruba1 285 KELARAFESFPGDADQIYPGWRKALGV 311 HHsearch alignment (Probability: 0.76 E-value:0.01) d1q6oa_ 12 TMDSAYETTRLIAEEVDIIEVGTILCVG----E------GVRAVRDLKALYPHKIVLADA 61 :::::::::::::::::::::::::::: : :::::::::::: :::::::: d5ruba1 35 RPKPFAEACHAFWLGGDFIKNDEPQGNQPFAPLRDTIALVADAMRRAQDET-GEAKLFSA 93 d1q6oa_ 62 K-IADAGKILSRM---CFEANAD-----WVTVICC-ADINTAKGALDVAKEFNG---DVQ 108 : ::::::::::: ::::::: ::::::: :::::::::::::::::: ::: d5ruba1 94 NITADDPFEIIARGEYVLETFGENASHVALLVDGYVAGAAAITTARRRFPDNFLHYHRAG 153 d1q6oa_ 109 I-ELT------GYWTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSD-- 159 : ::: ::::::::::::::::::::::::::: ::: :::::::::::::: d5ruba1 154 HGAVTSPQSKRGYTAFVHCKMARLQGASGIHTGTSSDR-AIA--YMLTQDEAQGPFYRQS 210 d1q6oa_ 160 ----MGFKVTVTGGLALEDLPLFKG-IP-IHVF-IAGRSIRDAAS-PVEAARQFKRSIAE 211 ::::::::::::::::::::: :: :::: ::::::::::: :::::::::::::: d5ruba1 211 WGGMKACTPIISGGMNALRMPGFFENLGNANVILTAGGGAFGHIDGPVAGARSLRQAWQA 270