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: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.883 --> Intermediate <-- 0.805 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1uwka_) through the intermediate protein (d1vi2a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1vi2a1 Putative shikimate dehydrogenase YdiBNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β
Hit d1uwka_ Urocanate hydratase HutUUrocanase (Pfam 01175)Urocanase (Pfam 01175)multi

Supporting Alignments

Query <-- 0.883 --> Intermediate
DALI alignment (Z-score: 4.6 Raw score:365.80) query 1 --------------GMENKKMNLLLfsgdydkALASLIIANAAREMEI-EVTIFCAFWgl 45 ::::::::::: :::::::::::::::: ::::::::: d1vi2a1 1 dgtghiraikesgfDIKGKTMVLLG------aGGASTAIGAQGAIEGLkEIKLFNRRD-- 52 query 46 LLLRdpekasqedkslyeqafssltpreaeelplskmnlggigkkmllemmkeekapkls 105 :::: d1vi2a1 53 EFFD-------------------------------------------------------- 56 query 106 dlLSGARKKE------VKFYAXQlsveimgfkkeelfpevqimDVKEYLKNALESDLQLF 159 :::::::: ::::::: ::::::::::::::::: d1vi2a1 57 kaLAFAQRVNentdcvVTVTDLA--------------------DQQAFAEALASADILTN 96 query 160 ------------------------------------------------------------ 160 d1vi2a1 97 gtkvgmkpleneslvndisllhpgllvtecvynphmtkllqqaqqagcktidgygmllwq 156 query 160 -------------------------i 160 d1vi2a1 157 gaeqftlwtgkdfpleyvkqvmgfga 182 FAST alignment (Normalized score: 4.17 Raw score:711.70) query 1 --------------GMENKKMNLLLFSGDYDK---ALASLIIANAAREME-IEVTIFCA- 41 ::::::::: ::::::::::::::: :::::::: d1vi2a1 1 DGTGHIRAIKESGFDIKGKTMVL---------LGAGGASTAIGAQGAIEGLKEIKLFNRR 51 query 42 FWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKA 101 ::::: d1vi2a1 52 DEFFD------------------------------------------------------- 56 query 102 PK-LSDLLSGARK---KEVKFYAXQLSVEIMGFKKEELFPEVQIM--DVKEYLKNALESD 155 :::::::::: ::::::: ::::::::::::: d1vi2a1 57 --KALAFAQRVNENTDCVVTVTD----------------------LADQQAFAEALASAD 92 query 156 LQLFI------------------------------------------------------- 160 ::: d1vi2a1 93 ILT--NGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQAGCKTIDGY 150 query 161 -------------------------------- 161 d1vi2a1 151 GMLLWQGAEQFTLWTGKDFPLEYVKQVMGFGA 182 TMalign alignment (TM-score: 0.31 Raw score:49.46) query 1 ------GMENKKMNL------------LLFSGDYD-KALASLIIAN-AAR--EMEIEVTI 38 :::: ::::: :::::::::: ::: d1vi2a1 1 DGTGHI-----RAIKESGFDIKGKTMV---LLGAGGASTAIGAQGAIEGLKE-------- 44 query 39 FCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKE 98 ::::::::: : ::::::::::::: d1vi2a1 45 ----------------------------------IKLFNRRDE-F--FDKALAFAQRVNE 67 query 99 EK-APKLS------------DLLSGARKKEVKFYA----XQLS----VEIMG--FKKEEL 135 :: ::::: ::::: : ::: : :::: :::::: d1vi2a1 68 NTDCVVTVTDLADQQAFAEA--LASAD---I-LTNGTKV---GMKPL-ENESLVNDISLL 117 query 136 FPEV-Q---------------IMD-----VKEYLKNALESDLQL---------------- 158 :::: : ::: ::: ::: ::::: d1vi2a1 118 HPGLLVTECVYNPHMTKLLQQAQQAGCKT--IDG-YGM-LLWQGAEQFTLWTGKDFPLEY 173 query 159 ---------FI 160 d1vi2a1 174 VKQVMGFGA-- 182 HHsearch alignment (Probability: 0.01 E-value:0.14) query 102 PKLSDLLSGARKKEVKFY 119 :::::::::::::::::: d1vi2a1 130 PHMTKLLQQAQQAGCKTI 147
Intermediate <-- 0.805 --> Hit
DALI alignment (Z-score: 8.4 Raw score:675.70) d1vi2a1 1 ------------------------------------------------------------ 1 d1uwka_ 1 nnkyrdveiraprgnkltakswlteaplrmlmnnldpqvaenpkelvvyggigraarnwe 60 d1vi2a1 1 ------------------------------------------------------------ 1 d1uwka_ 61 cydkivetltrleddetllvqsgkpvgvfkthsnaprvliansnlvphwanwehfnelda 120 d1vi2a1 1 ------------------------DGTGHIRAIKESGF--DIKGKTMVLLGAGGASTAIG 34 :::::::::::::: :::::::::::::::::::: d1uwka_ 121 kglamygqmtagswiyigsqgivqGTYETFVEAGRQHYggSLKGKWVLTAGLGGMGGAQP 180 d1vi2a1 35 AQGAIEGLkEIKLFNRRDEFFDKAL--AFAQR--------------vnentDCVVTVTDL 78 :::::::: :::::::::::::::: ::::: ::::::::: d1uwka_ 181 LAATLAGA-CSLNIESQQSRIDFRLetRYVDEqatdlddalvriakytaegKAISIALHG 239 d1vi2a1 79 AdQQAFAEA---lASADILTNGTKVGMKP---------------------------LENE 108 : ::::::: :::::::::::::::: :::: d1uwka_ 240 NaAEILPELvkrgVRPDMVTDQTSAHDPLngylpagwtweqyrdraqtepaavvkaAKQS 299 d1vi2a1 109 S--LVNDisLLHP-GLLVTECVynphmtKLLQ--------QAQQagcKTIDGYGM----- 152 : :::: :::: :::::::: :::: :::: :::::::: d1uwka_ 300 MavHVQAmlDFQKqGVPTFDYG-----nNIRQmakeegvaDAFD---FPGFVPAYirplf 351 d1vi2a1 153 ------------------------------------------------------------ 153 d1uwka_ 352 crgvgpfrwaalsgeaediyktdakvkelipddahlhrwldmarerisfqglparicwvg 411 d1vi2a1 153 ------------------------------------------------------------ 153 d1uwka_ 412 lglraklglafnemvrsgelsapvvigrdhldsgsvsspnaeteamrdgsdavsdwplln 471 d1vi2a1 153 -----------------------------------------------------llwqgae 159 d1uwka_ 472 allntaggatwvslhhgggvgmgfsqhsgmvivcdgtdeaaeriarvltndpgtgvmrha 531 d1vi2a1 160 qftlwtgkdfpleyvkqvmgfga 182 d1uwka_ 532 dagydiaidcakeqgldlpmitg 554 FAST alignment (Normalized score: 3.54 Raw score:1122.00) d1vi2a1 1 D----------------------------------------------------------- 1 d1uwka_ 1 -NNKYRDVEIRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAARNW 59 d1vi2a1 2 ------------------------------------------------------------ 2 d1uwka_ 60 ECYDKIVETLTRLEDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNELD 119 d1vi2a1 2 -----------------------GTGHIRAIKE-----SGFDIKGKTMVLLGAGGASTAI 33 :::::::::: :::::::::::::::::::::: d1uwka_ 120 AKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYGGSLKGKWVLTAGLGGMGGAQ 179 d1vi2a1 34 GAQGAIEGLKEIKLFNR-RDEFFDKALAFAQRVNENT----------------------- 69 :::::::: ::::::: :::::::::: d1uwka_ 180 PLAATLAG-ACSLNIE-SQQSRIDFRLE---------TRYVDEQATDLDDALVRIAKYTA 228 d1vi2a1 70 --DCVVTVTDLAD----QQAFAEAL---ASADILTNGTKVGMK----------------- 103 ::::::: :::::::: :::::::::: d1uwka_ 229 EGKAISIAL----HGNAAEILPELVKRGVRPDMVTDQT-----SAHDPLNGYLPAGWTWE 279 d1vi2a1 104 ---------------PLENESLVNDISLLHPGLLVTECVYNPHM-----TKLLQQAQQAG 143 :::: ::::::::::: d1uwka_ 280 QYRDRAQTEPAAVVKAAKQ-------------------------SMAVHVQAMLDFQKQG 314 d1vi2a1 144 CKTIDGYGML-------------------------LWQGAEQFTLWTGKDFPLEYVKQVM 178 ::::: :::::::: d1uwka_ 315 VPTFD-----YGNNIRQMAKEEGVADAFDFPGFVPAYIRPLFC----------------- 352 d1vi2a1 179 GFGA-------------------------------------------------------- 182 d1uwka_ 353 ----RGVGPFRWAALSGEAEDIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARIC 408 d1vi2a1 183 ------------------------------------------------------------ 183 d1uwka_ 409 WVGLGLRAKLGLAFNEMVRSGELSAPVVIGRDHLDSGSVSSPNAETEAMRDGSDAVSDWP 468 d1vi2a1 183 ------------------------------------------------------------ 183 d1uwka_ 469 LLNALLNTAGGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGVM 528 d1vi2a1 183 -------------------------- 183 d1uwka_ 529 RHADAGYDIAIDCAKEQGLDLPMITG 554 TMalign alignment (TM-score: 0.64 Raw score:116.50) d1vi2a1 1 ------------------------------------------------------------ 1 d1uwka_ 1 NNKYRDVEIRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAARNWE 60 d1vi2a1 1 ------------------------------------------------------------ 1 d1uwka_ 61 CYDKIVETLTRLEDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNELDA 120 d1vi2a1 1 ---------------------DGTGHIRAIKES--GFD--IKG-KTMVLLGAGGASTAIG 34 :::::::::::: ::: ::: :::::::::::::::: d1uwka_ 121 KGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYGGSLKGKWVLTAGLGGMGGAQP 180 d1vi2a1 35 AQGAIEGLKEIKLFNRRDEFFDKALA---FAQR---------VN-------ENTDCVVTV 75 :::::::: ::::::::::::::::: :::: : ::::::: d1uwka_ 181 LAATLAGA-CSLNIESQQSRIDFRLETRYVDEQATDLDDALV-RIAKYTAE--GKAISIA 236 d1vi2a1 76 TDLAD-QQAFAEA--LASADILTNGTKVGMKPL------------------------E-- 106 ::::: ::::::: ::::::::::::: :::: : d1uwka_ 237 LHGNAAEILPELVKRGVRPDMVTDQTSA-HDPLNGYLPAGWTWEQYRDRAQTEPAAVVKA 295 d1vi2a1 107 -N-ESLVNDISL-LH-P-GLLVTECVYNPHMTKLLQ--QAQQAGCKTIDGYGMLL-WQ-- 156 : ::::::::: :: : ::::::::: :::::::: :::::: :::::::::: :: d1uwka_ 296 AKQSMAVHVQAMLDFQKQGVPTFDYGN-NIRQMAKEEGVADAFD-FPGFVPAYIRPLFCR 353 d1vi2a1 157 -GAEQ--------------------------------------------------FTLWT 165 :::: ::::: d1uwka_ 354 GVGPFRWAALSGEAEDIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLG 413 d1vi2a1 166 GK---------------------------DFPLEYVKQVMG-----F-------GA---- 182 :: ::: ::: : :: d1uwka_ 414 LRAKLGLAFNEMVRSGELSAPVVIGRDHL-----DSG-SVSSPNAETEAMRDGSDAVSDW 467 d1vi2a1 183 ------------------------------------------------------------ 183 d1uwka_ 468 PLLNALLNTAGGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGV 527 d1vi2a1 183 --------------------------- 183 d1uwka_ 528 MRHADAGYDIAIDCAKEQGLDLPMITG 554 HHsearch alignment (Probability: 0.09 E-value:0.01) d1vi2a1 5 HIRAI-KESGFDIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFF 55 ::::: :::::::::::::::::::::::::::::::::::: ::::::::: d1uwka_ 150 FVEAGRQHYGGSLKGKWVLTAGLGGMGGAQPLAATLAGACSL-NIESQQSRI 200