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 <-- 0.820 --> Intermediate <-- 0.673 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1nria_) through the intermediate protein (d1vhca_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1vhca_ Hypothetical protein HI0047AldolaseTIM beta/​alpha-​barrelα/β
Hit d1nria_ Hypothetical protein HI0754SIS domainSIS domainα/β

Supporting Alignments

Query <-- 0.820 --> Intermediate
DALI alignment (Z-score: 9.5 Raw score:878.00) query 1 ----------mietpyylidkakLTRNMERIAHVREKSGA-KALLALKCFatWSVFDLMR 49 ::::::::::::::::: ::::::::: :::::::: d1vhca_ 1 syttqqiieklrelkivpvialdNADDILPLADTLAKNGLsVAEITFRSEaaADAIRLLR 60 query 50 ----DYMDGTTSSSL-FEVRLGRERFGKETHAYSvaYGDNEIDEVV--SHADKIIFNSIS 102 ::::::::::: :::::::::::::::::: :::::::::: :::::::::::: d1vhca_ 61 anrpDFLIAAGTVLTaEQVVLAKSSGADFVVTPG--LNPKIVKLCQdlNFPITPGVNNPM 118 query 103 QLERFADKAAgiARGLRLNPqrLGEW--DVPKVER-VMDRINGFMIHNncenkdfglfdr 159 :::::::::: :::::::: :::: ::::::: :::::::::::: d1vhca_ 119 AIEIALEMGI-sAVKFFPAE--ASGGvkMIKALLGpYAQLQIMPTGGI------------ 163 query 160 MLGEIEeRFGALiARVDWVSLG--gGIHFTGDdYPVDAFSARLRAFSDRYGvqiylepge 217 :::::: ::::: ::::::::: ::::::: :::::::::::::::::: d1vhca_ 164 GLHNIR-DYLAI-PNIVACGGSwfvEKKLIQS-NNWDEIGRLVREVIDIIK--------- 211 query 218 asitksttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsymicgks 277 d1vhca_ 212 ------------------------------------------------------------ 212 query 278 clagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvre 337 d1vhca_ 212 ------------------------------------------------------------ 212 query 338 ftyadyeqsls 348 d1vhca_ 212 ----------e 212 FAST alignment (Normalized score: 4.72 Raw score:1281.00) query 1 MIETPYYLIDKAK----------------------------------------------- 13 d1vhca_ 1 -------------SYTTQQIIEKLRELKIVPVIALDNADDILPLADTLAKNGLSVAEITF 47 query 14 -LTRNMERIAHVREK-SGAKALLALK-CFATWSVFDLMRD-YMDGTTSSS--LFEVRLGR 67 :::::::::::::: ::::::: ::::::::::::: ::::::::: :::::::: d1vhca_ 48 RSEAAADAIRLLRANRPDFLIAA---GTVLTAEQVVLAKSSGADFVVTPGLNPKIVKLCQ 104 query 68 ERFGKETHAYSVAYGDNEIDEVVS-HADKIIFN------SISQLERFADKAAGIARGLRL 120 :::::::::: ::::::::::: :::::::: :::::::::::::::::::: d1vhca_ 105 -DLNFPITPGV--NNPMAIEIALEMGISAVKFFPAEASGGVKMIKALLGPYAQLQIMPT- 160 query 121 NPQRLGEW---DVPKVERV--MDRINGFMIHNNCEN---------KDFGLFDRMLGEIEE 166 :::::::: ::::::::::: ::::::::::::::: d1vhca_ 161 --------GGIGLHNIRDYLAIPNIVACGGSW----FVEKKLIQSNNWDEIGRLVREVID 208 query 167 RFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEASITKSTTL 226 :: d1vhca_ 209 II---------------------------------------------------------- 210 query 227 EVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGE 286 d1vhca_ 211 ------------------------------------------------------------ 211 query 287 FRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQS 346 d1vhca_ 211 ------------------------------------------------------------ 211 query 347 LS-- 348 d1vhca_ 211 --KE 212 TMalign alignment (TM-score: 0.42 Raw score:147.60) query 1 ----------------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKC 38 : :::::::::::::::::::::::::: d1vhca_ 1 SYTTQQIIEKLRELKIVPVIAL---------D--NADDILPLADTLAKNGLSVAEITFRS 49 query 39 FATWSVFDLMR-DY--M-DGTTSSSLF-EVRLGRERFGKETHAYSVAYGDNEIDEVVSH- 92 ::::::::::: :: : ::::::::: :::::: :::::::::::::: ::::::::: d1vhca_ 50 EAAADAIRLLRANRPDFLIAAGTVLTAEQVVLAK-SSGADFVVTPGLNP-KIVKLCQDLN 107 query 93 ADKIIFNSI-SQLERFADKAAGIARGLRLNPQRLGEW--DVPKVER-VMDRINGFMIHNN 148 ::::::::: ::::::::::: :::::::::: ::: ::::::: :::: :::::::: d1vhca_ 108 FPITPGVNNPMAIEIALEMGI-SAVKFFPAEA--SGGVKMIKALLGPYAQL-QIMPTGGI 163 query 149 CENKDFGLFDRMLGEIEERFGALIARVDWVSLGG-GIH-FT-GDD-YPVDAFSARLRAFS 204 ::::::: :::: :::::::::: ::: :: ::: :::::::::::::: d1vhca_ 164 -----------GLHNIRD-YLAI-PNIVACGGSWFVEKKLIQSNNWDEIGRLVREVIDII 210 query 205 DRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLP 264 :: d1vhca_ 211 KE---------------------------------------------------------- 212 query 265 NEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIA 324 d1vhca_ 213 ------------------------------------------------------------ 213 query 325 IRELDGSVRTVREFTYADYEQSLS 348 d1vhca_ 213 ------------------------ 213 HHsearch alignment (Probability: 0.41 E-value:0.01) query 15 TRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKET 74 ::::::::::::: ::::::::::::::::::::::::::::::::::::::::::: d1vhca_ 53 ADAIRLLRANRPD----FLIAAGTVLTAEQVVLAKSSGADFVVTPGLNPKIVKLCQDLNF 108 query 75 HAYSVAYGDNEIDEVVSHADKII-------FNSISQLERFADKAAGIARGLRLNPQRLGE 127 ::::::::::::::::::::::: :::::::::::::::::::: :::: d1vhca_ 109 PITPGVNNPMAIEIALEMGISAVKFFPAEASGGVKMIKALLGPYAQLQIM------PTGG 162 query 128 WDVPKVERVMDRINGFMIHNNCENK--------DFGLFDRMLGEIEERFGA 170 :::::::::: :::::::::::::: :::::::::::::::::: d1vhca_ 163 IGLHNIRDYL-AIPNIVACGGSWFVEKKLIQSNNWDEIGRLVREVIDIIKE 212
Intermediate <-- 0.673 --> Hit
DALI alignment (Z-score: 2.8 Raw score:400.50) d1vhca_ 1 ------------------------------------------syTTQQIIEKLRELK--- 15 ::::::::::::: d1nria_ 1 lstliteqrnpnsvdidrqstleivrlmneedklvplaiesclpQISLAVEQIVQAFqqg 60 d1vhca_ 16 -IVPVIA--------------------------------------------LDNADDILP 30 :::::: ::::::::: d1nria_ 61 gRLIYIGagtsgrlgvldasecpptfgvstemvkgiiaggecairhpvegaEDNTKAVLN 120 d1vhca_ 31 LADTLAknglSVAEITF---RSEAAADAIRLLRAnrPDFLIAAGtVLTAEQvvLAKSsGA 87 :::::: ::::::: :::::::::::::: :::::::: :::::: :::: :: d1nria_ 121 DLQSIHfsknDVLVGIAasgRTPYVIAGLQYAKS--LGALTISI-ASNPKS--EMAE-IA 174 d1vhca_ 88 DFVVTPGLNPKivklcqdlnfpitpgvnnpmaieialemgisavkffpaeasggvkmika 147 ::::::::::: d1nria_ 175 DIAIETIVGPE---------------------------------------iltgssrlks 195 d1vhca_ 148 llgpyaqlQIMPtggiglhnirdYLAIPnivacggswfvekkliqsnnwdeigrlvrevi 207 :::: ::::: d1nria_ 196 gtaqkmvlNMLT------tasmiLLGKC------yenlmvdvqasneklkaravrivmqa 243 d1vhca_ 208 diike 212 d1nria_ 244 tdcnk 248 FAST alignment (Normalized score: 3.17 Raw score:726.50) d1vhca_ 1 SY--------------------------------------------TTQQIIEKLREL-- 14 ::::::::::: d1nria_ 1 --LSTLITEQRNPNSVDIDRQSTLEIVRLMNEEDKLVPLAIESCLPQISLAVEQIVQ-AF 57 d1vhca_ 15 ---KIVPVIA---------------------------------------------LDNAD 26 :::::: ::::: d1nria_ 58 QQGGRLIYI-GAGTSGRLGVLDASECPPTFGVSTEMVKGIIAGGECAIRHPVEGAEDNTK 116 d1vhca_ 27 DILPLADTLAKNGL------SVAEITF---RSEAAADAIRLLRANRPDFLIAAGTVLTAE 77 :::::::: ::::::: :::::::::::::: ::::::: ::::: d1nria_ 117 AVLNDLQS------IHFSKNDVLVGIAASGRTPYVIAGLQYAKS--LGALTIS-IASNP- 166 d1vhca_ 78 QV-VLAKSSGADFVVTPGLNPKIVKLCQDLNFPITPGVNNPMAIEIALEMGISAVKFFPA 136 ::::: :::::::::: d1nria_ 167 --KSEMAE-IADIAIETIV----------------------------------------- 182 d1vhca_ 137 EASGGVKMIKALLGPYAQLQIMPTGGIGLHNIRDYLAIPNIVACGGSWFVEKKLIQSNNW 196 d1nria_ 183 ------------------------------------------------------------ 183 d1vhca_ 197 DEIGRLVREVIDIIKE-------------------------------------------- 212 d1nria_ 183 ----------------GPEILTGSSRLKSGTAQKMVLNMLTTASMILLGKCYENLMVDVQ 226 d1vhca_ 213 ---------------------- 213 d1nria_ 227 ASNEKLKARAVRIVMQATDCNK 248 TMalign alignment (TM-score: 0.36 Raw score:76.64) d1vhca_ 1 ------------------------------------------------SYTT-QQIIEKL 11 : ::::::: d1nria_ 1 LSTLITEQRNPNSVDIDRQSTLEIVRLMNEEDKLVPLAIESCLPQISL---AVEQIVQAF 57 d1vhca_ 12 -------RELKIV--------PVIA-LDNADDILPLADTLAKNGLS---VAEITFRSEAA 52 : :::: : :: ::::::: ::::::::::: d1nria_ 58 QQGGRLI-----YIGAGTSGRLGVLD------A--SE--CPPTFGVSTEMVKGIIAGGEC 102 d1vhca_ 53 ---------ADAIRLLRANRPDFLIAAGTVLTAEQVVLAKSSGA---DFV-VTP--GL-N 96 :::::::::::::::: ::: ::: :: : d1nria_ 103 AIRHPVEGA-------------------EDNTKAVLNDLQSIHFSKNDVLVGIAASGRTP 143 d1vhca_ 97 --PKIVKLCQDLNFPITPGVNNPMAIEIALEMGISAVKF-F--------PAEASGGVKMI 145 ::::::::::::::::::::::: :::::::::::: : ::::::: d1nria_ 144 YVIAGLQYAKSLGALTISIASNPKS--EMAEIADIAIETIVGPEILTGSSRLKSGT---- 197 d1vhca_ 146 KALLGPYAQLQIMPTGGIGLHNIRDYLAIPNIVACG------------------GSWFVE 187 ::: : :: ::::: d1nria_ 198 -------------AQK-M-------VL----NMLTTASMILLGKCYENLMVDVQ------ 226 d1vhca_ 188 KKLIQSNNWDEIGR-LVR------------EVIDIIKE 212 ::::::: :: d1nria_ 227 -------ASNEKLKA-RAVRIVMQATDCNK-------- 248 HHsearch alignment (Probability: 0.01 E-value:0.31) d1vhca_ 106 LNFPITPGVNNP-------MAIEIALEMGISAVKFF 134 :::::::::::: ::::::::::::::::: d1nria_ 128 SKNDVLVGIAASGRTPYVIAGLQYAKSLGALTISIA 163