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 <-- 1.321 --> Intermediate <-- 1.212 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1rcqa1) through the intermediate protein (d1knwa1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1knwa1 Diaminopimelate decarboxylase LysAAlanine racemase C-​terminal domain-​likeDomain of alpha and beta subunits of F1 ATP synthase-​likeAll β
Hit d1rcqa1 Alanine racemaseAlanine racemase C-​terminal domain-​likeDomain of alpha and beta subunits of F1 ATP synthase-​likeAll β

Supporting Alignments

Query <-- 1.321 --> Intermediate
DALI alignment (Z-score: 15.0 Raw score:988.00) query 1 ---------------------MIETPYYLIdkakltrnmeriahvreksgakallalkcf 39 ::::::::: d1knwa1 1 phslfstdtdltaenllrlpaEFGCPVWVY------------------------------ 30 query 40 atwsvfdlmrdymdgttssslfevrlgrerfgkethaysvaygdneidevvshadkiifn 99 d1knwa1 31 ------------------------------------------------------------ 31 query 100 sisqlerfadkaagiarglrlnpqrlgewdvpkvervmdringfmihnncenkdfglfdr 159 d1knwa1 31 ------------------------------------------------------------ 31 query 160 mlgeieerfgaliarvdwvslgggihftgddypvdafsarlrafsdrygvqiylepgeas 219 d1knwa1 31 ------------------------------------------------------------ 31 query 220 itkstTLEVTVLDTLYN--KNLAIVDSSIeAHMLDLLIYRETAKVL---------pneGS 268 :::::::::::: :::::::::: :::::::::::::::: :: d1knwa1 31 -----VLITQVRSVKQMgsRHFVLVDAGF-NDLMRPAMYGSYHHISalaadgrslehaPT 84 query 269 HSYMICGKSCLAGDVFG--------EFRFaEELKVGDRISFQDAAGYTMVKKNWFNGVKM 320 ::::::::::::::::: :::: :::::::::::::::::::::::::::::: d1knwa1 85 VETVVAGPLCESGDVFTqqeggnveTRAL-PEVKAGDYLVLHDTGAYGASMSSNYNSRPL 143 query 321 PAIAIRELdGSVRTVREFTYadYEQSLS------ 348 :::::::: ::::::::::: :::::: d1knwa1 144 LPEVLFDN-GQARLIRRRQT--IEELLAlellhh 174 FAST alignment (Normalized score: 8.04 Raw score:1978.00) query 1 ---------------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF 39 ::::::: d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVW-------------------------------- 28 query 40 ATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFN 99 d1knwa1 29 ------------------------------------------------------------ 29 query 100 SISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDR 159 d1knwa1 29 ------------------------------------------------------------ 29 query 160 MLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEAS 219 d1knwa1 29 ------------------------------------------------------------ 29 query 220 ITKS-TTLEVTVLDTLYN----KNLAIVDSSIEAHMLDLLIYRETAKVLPNEG------- 267 ::::::::::: ::::::::: :::::::::::::::: d1knwa1 29 ----VYVLITQVRSVK--QMGSRHFVLVDAG-FNDLMRPAMYGSYHHI-----SALAADG 76 query 268 -------SHSYMICGKSCLAGDV--------FGEFRFAEELKVGDRISFQDAAGYTMVKK 312 :::::::::::::::: :::::: :::::::::::::::::::::: d1knwa1 77 RSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRAL-PEVKAGDYLVLHDTGAYGASMS 135 query 313 NWFNGVKMPAIAIRELDGSVRTV-REFTYADYEQSLS----- 348 ::::::::::::::: ::::::: ::::::::::: d1knwa1 136 SNYNSRPLLPEVLFD-NGQARLIRRRQTIEELLAL--ELLHH 174 TMalign alignment (TM-score: 0.35 Raw score:120.59) query 1 ---------------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF 39 ::::::::: d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVWVY------------------------------ 30 query 40 ATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFN 99 d1knwa1 31 ------------------------------------------------------------ 31 query 100 SISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDR 159 d1knwa1 31 ------------------------------------------------------------ 31 query 160 MLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEAS 219 d1knwa1 31 ------------------------------------------------------------ 31 query 220 ITKSTTLEVTVLDTLYN--KNLAIVDSSIEAHMLDLLIYRETAKVLP--------NE-GS 268 :::::::::::: :::::::::: ::::::::::::::::: :: :: d1knwa1 31 -----VLITQVRSVKQMGSRHFVLVDAGF-NDLMRPAMYGSYHHISALAADGRSLEHAPT 84 query 269 HSYMICGKSCLAGDVFG--------EFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKM 320 ::::::::::::::::: ::::: ::::::::::::::::::::::::::::: d1knwa1 85 VETVVAGPLCESGDVFTQQEGGNVETRALP-EVKAGDYLVLHDTGAYGASMSSNYNSRPL 143 query 321 PAIAIRELDGSVRTVRE-FTYADYEQSLS--- 348 :::::::: :::::::: ::::::::::: d1knwa1 144 LPEVLFDN-GQARLIRRRQTIEELLALELLHH 174 HHsearch alignment (Probability: 1.00 E-value:0.00) query 193 VDAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLD 252 ::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::: d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVWVYVLITQVRSVKQMGSRHFVLVDAGFN-DLMR 59 query 253 LLIYRETAKVLP---------NEGSHSYMICGKSCLAGDVFGEF-------RFAEELKVG 296 :::::::::::: ::::::::::::::::::::::: ::::::::: d1knwa1 60 PAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRALPEVKAG 119 query 297 DRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQS 346 :::::::::::::::::::::::::::::::::::::::::::::::::: d1knwa1 120 DYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLAL 169
Intermediate <-- 1.212 --> Hit
DALI alignment (Z-score: 4.1 Raw score:359.70) d1knwa1 1 phslfstdtdltaenllrlpaefGCPVWVyVLITQVRSVKQMGS---------------R 45 :::::: :::::::::::::: : d1rcqa1 1 ----------------------mRPARAL-TLESKVISVRDLPAgepvgygarysterrQ 37 d1knwa1 46 HFVLVDAGFNDLMRpAMYGsyhHISALaadgrslehaptvetvvagplceSGDVftqqeg 105 :::::::::::::: :::: ::::: :::: d1rcqa1 38 RIGVVAMGYADGYP-RHAAdgtLVFID----------------gkpgrlvGRVS---mdm 77 d1knwa1 106 gnvetrALPEVKAGDYLVLHD--------------tgAYGASMSSnynsrpLLPEVLFDN 151 ::::::::::::::: :::::::: ::::::::: d1rcqa1 78 ltvdltDHPQAGLGSRVELWGpnvpvgalaaqfgsipYQLLCNLK------RVPRVYSGA 131 d1knwa1 152 gqarlirrrqtieellalellhh 174 d1rcqa1 132 ----------------------- 132 FAST alignment (Normalized score: 3.45 Raw score:521.40) d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEF-GCPVWVYVLITQVRSVKQMG---------------- 43 :::: :::::::::::::: d1rcqa1 1 -----------------------MRPAR-ALTLESKVISVRDL-PAGEPVGYGARYSTER 35 d1knwa1 44 SRHFVLVDAGFNDLMRPAMYG--------SYHHISALAADGRSLEHAPTVETVVAGPLCE 95 :::::::::::: :::::: d1rcqa1 36 RQRIGVVAMGYA---------DGYPRHAADGTLVF------------------------- 61 d1knwa1 96 SGDVFTQQEGGNVETRAL------------------------PEVKAGDYLVLHDT---- 127 ::::::::::: d1rcqa1 62 ------------------IDGKPGRLVGRVSMDMLTVDLTDHPQAGLGSRVEL---WGPN 100 d1knwa1 128 -------------GAYGASMSSNYNSRP-LLPEVLFDNGQARLIRRRQTIEELLALELLH 173 :::::::: ::::::: d1rcqa1 101 VPVGALAAQFGSIPYQLLCNL-------KRVPRVYS------------------------ 129 d1knwa1 174 H-- 174 d1rcqa1 130 -GA 131 TMalign alignment (TM-score: 0.42 Raw score:72.62) d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVWVYVLITQVRSVKQMGS-----------R---H 46 : :::::: :::::::::::::: : : d1rcqa1 1 -------------------M---RPARAL-TLESKVISVRDLPAGEPVGYGARYSTERRQ 37 d1knwa1 47 -FVLVDAGFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEG 105 ::::::::::::: :::::::::::: :: ::::::::::: :::: d1rcqa1 38 RIGVVAMGYADGYP-RHAADGTLVFID------GK---PGRLVGRVSMD---MLTV---- 80 d1knwa1 106 GNVETRALPE-VKAGDYLVLH----DT----------GAYGASMSSNYNSRPLLPEVLFD 150 :::::: :::::::::: :: ::::::::: :::::::: d1rcqa1 81 ----DLTDHPQAGLGSRVELWGPNVPVGALAAQFGSIPYQLLCNLK------RVPRVYSG 130 d1knwa1 151 NGQARLIRRRQTIEELLALELLHH 174 : d1rcqa1 131 --A--------------------- 131 HHsearch alignment (Probability: 0.37 E-value:0.01) d1knwa1 42 MGSRHFVLVDAGFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFT 101 :::::::::::::::::::::::::: ::: :::::::::::::::::: d1rcqa1 34 ERRQRIGVVAMGYADGYPRHAADGTL---VFI---------DGKPGRLVGRVSMDMLTV- 80 d1knwa1 102 QQEGGNVETRALPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFD 150 :: ::::::::::::::::::::::::::::::: ::::::: d1rcqa1 81 -DL------TDHPQAGLGSRVELWGPNVPVGALAAQFGSI--PYQLLCN 120