HorA Server Transitive Detail

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


Query <-- 1.541 --> Intermediate <-- 1.431 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1uhva2) through the intermediate protein (d1q6oa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1q6oa_ 3-​keto-​L-​gulonate 6-​phosphate decarboxylaseRibulose-​phoshate binding barrelTIM beta/​alpha-​barrelα/β
Hit d1uhva2 Beta-​D-​xylosidase,​ catalytic domain(Trans)glycosidasesTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 1.541 --> Intermediate
DALI 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 <-- 1.431 --> Hit
DALI alignment (Z-score: 9.8 Raw score:1070.10) d1q6oa_ 1 --LPML-QVALDN-QTMDS--AYETTRLIAE--EVDIIEvGTILCV-GEGV--------- 42 :::: :::::: ::::: :::::::::: :::::: :::::: :::: d1uhva2 1 fsDRWRyCVGTGRlGLALQkeYIETLKYVKEniDFKYIR-GHGLLCdDVGIyredvvgde 59 d1q6oa_ 43 -------raVRDLKALYP--HKIVLADAK------------------------iadAGKI 69 ::::::::: ::::::::: :::: d1uhva2 60 vkpfynftyIDRIFDSFLeiGIRPFVEIGfmpkklasgtqtvfywegnvtppkdyeKWSD 119 d1q6oa_ 70 LSRMCFEAN----------aDWVTVI-------------ccADINTAKGALDVAKEFN-- 104 ::::::::: :::::: ::::::::::::::::: d1uhva2 120 LVKAVLHHFisrygieevlkWPFEIWnepnlkefwkdadekEYFKLYKVTAKAIKEVNen 179 d1q6oa_ 105 GDVQIELT--GYWT--WEQAQQWR--DAGIGQVVYHRSrdaQAAG--------------- 143 :::::::: :::: :::::::: :::::::::::: :::: d1uhva2 180 LKVGGPAIcgGADYwiEDFLNFCYeeNVPVDFVSRHAY---TSKQgeytphliyqeimps 236 d1q6oa_ 144 vAWGEADITAIKRLSD---MGFKVT-VTGG-----------------lALEDLPLFKGIp 182 ::::::::::::::: :::::: :::: ::::::::::: d1uhva2 237 eYMLNEFKTVREIIKNshfPNLPFHiTEYNtsyspqnpvhdtpfnaayIARILSEGGDY- 295 d1q6oa_ 183 IHVFIAGrSIRD---------------------aASPVEAARQFKRSiAELW- 213 ::::::: :::: ::::::::::::: :::: d1uhva2 296 VDSFSYW-TFSDvfeerdvprsqfhggfglvalnMIPKPTFYTFKFF-NAMGe 346 FAST alignment (Normalized score: 6.14 Raw score:1666.00) d1q6oa_ 1 LPM------LQVALDNQ-----------TMDSAYETTRLIAE-EVDIIEVGTILCVGEG- 41 :::: ::::::::::: ::::: d1uhva2 1 ---FSDRWRYCVG----TGRLGLALQKEYIETLKYVKEN---IDFKYI-----------R 39 d1q6oa_ 42 ------------------------------VRAVRDLKALYPHKIVLADAKIAD------ 65 ::::::::: ::::::: d1uhva2 40 GHGLLCDDVGIYREDVVGDEVKPFYNFTYIDRIFDSFLE--IGIRPFV------EIGFMP 91 d1q6oa_ 66 ------------------------AGKILSRMCFEANA-------------DWVTVICCA 88 ::::::::::: ::::: d1uhva2 92 KKLASGTQTVFYWEGNVTPPKDYEKWSDLVKAVLH---HFISRYGIEEVLKWPFEI---- 144 d1q6oa_ 89 -----------------DINTAKGALDVAKE--FNGDV-QIELTGYWTWEQAQQWRD--- 125 :::::::::::::: ::::: ::::::: :::::::::: d1uhva2 145 WNEPNLKEFWKDADEKEYFKLYKVTAKAIKEVNENLKVGGPAICGG-ADYWIEDFLNFCY 203 d1q6oa_ 126 ---AGIGQVVYHRSRDAQ---------------AAGVAWGEADITAIKRLSD-------M 160 ::::::::: ::::: ::::::::::::: : d1uhva2 204 EENVPVDFVSRH------AYTSKQGEYTPHLIYQEIMP-SEYMLNEFKTVREIIKNSHFP 256 d1q6oa_ 161 GFKVTVTGGL---------------------ALEDLPLFKGIPIHVFIAGRSIRDA---- 195 ::::::: :::::::::: :::::: d1uhva2 257 NLPFHIT---EYNTSYSPQNPVHDTPFNAAYIARILSEGGD-YVDSFS--------YWTF 304 d1q6oa_ 196 ---------------------------ASPVEAARQFKRSIAELW---- 213 ::::::::::: d1uhva2 305 SDVFEERDVPRSQFHGGFGLVALNMIPKPTFYTFKFFN-------AMGE 346 TMalign alignment (TM-score: 0.60 Raw score:127.62) d1q6oa_ 1 --L--PM----------------------------LQVAL-DN-Q---T----------- 12 : :: ::::: :: : : d1uhva2 1 FSDRWRYCVGTGRLGLALQKEYIETLKYVKENIDFKYIRGHGLLCDDVGIYREDVVGDEV 60 d1q6oa_ 13 -----MDSAYETTRLIAEEVDIIEVGTILCVG-------------------------E-- 40 ::::::::::::::::::::::: ::: : d1uhva2 61 KPFYNFTYIDRIFDSFLEIGIRPFVEIG-FMPKKLASGTQTVFYWEGNVTPPKDYEKWSD 119 d1q6oa_ 41 GV-RAVRDLKALY-PHK--IVLADAK--I-------------ADA-GKILSRMCFEAN-- 78 :: :::::::::: ::: ::::::: : ::: :::::::::::: d1uhva2 120 LVKAVLHHFISRYGIEEVLKWPFEIWNEPNLKEFWKDADEKEYFKLYKVTAKAIKEVNEN 179 d1q6oa_ 79 ADWVTVIC---C--ADINTAK-GA--LDVAKEFNGDVQIELTGY---------------- 114 :::::::: : ::::::: :: :::: ::::::::: d1uhva2 180 LKVGGPAICGGADYWIEDFLNFCYEENVPV-----DFVSRHAYTSKQGEYTPHLIYQEIM 234 d1q6oa_ 115 ----W-TW--EQAQQWRD---AGIGQVVYHRS-RDAQAAG-VA----WGEADITAIKRLS 158 : :: :::::::: ::::::::::: :::::: :: ::::::::::::: d1uhva2 235 PSEYMLNEFKTVREIIKNSHFPNLPFHITEYNT-SYSPQNPVHDTPFNAAYIARILSEGG 293 d1q6oa_ 159 DMGFKVTVTGGL-------------------AL-----E--DLPLF-KGIPIHVFIAGRS 191 :: ::::::::: :: : ::::: :: d1uhva2 294 DY-VDSFSYWTFSDVFEERDVPRSQFHGGFGLVALNMIPKPTFYTFKFF----------- 341 d1q6oa_ 192 IRDAASPVEAARQFKRSIAELW- 213 : ::: d1uhva2 342 -----------------N-AMGE 346 HHsearch alignment (Probability: 0.03 E-value:0.07) d1q6oa_ 93 AKGALDVAKEFNGDVQIEL 111 ::::::::::::::::::: d1uhva2 69 IDRIFDSFLEIGIRPFVEI 87