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: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.827 --> Intermediate <-- 0.943 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1p3y1_) through the intermediate protein (d1jmva_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jmva_ Universal stress protein A,​ UspAAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1p3y1_ MrsDHomo-​oligomeric flavin-​containing Cys decarboxylases,​ HFCDHomo-​oligomeric flavin-​containing Cys decarboxylases,​ HFCDα/β

Supporting Alignments

Query <-- 0.827 --> Intermediate
DALI alignment (Z-score: 7.9 Raw score:512.80) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1jmva_ 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1jmva_ 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1jmva_ 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1jmva_ 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1jmva_ 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvglrayvaknGFRSVLIGLSGGIDSALVAAIACDALG--aqNVYGVS 358 ::::::::::::::::::::::::::: :::::: d1jmva_ 1 -----------------------MYKHILVAVDLSEESPILLKKAVGIAKrhdaKLSIIH 37 query 359 MPS------------------kysSDHSKGDAAELARRTG---lNFRTVSIepmfdayma 397 ::: :::::::::::::::: ::::::: d1jmva_ 38 VDVnfsdlytglidvnmssmqdriSTETQKALLDLAESVDypisEKLSGSG--------- 88 query 398 slgltglaeenlqsrLRGTTLMAISNQEGH-IVLAPGNKseLAVGYS------tlygdsv 450 ::::::::::::::: :::::::: :::::: d1jmva_ 89 ---------------DLGQVLSDAIEQYDVdLLVTGHHQ--DFWSKLmsstrqvmntiki 131 query 451 gAYGPiKDVYktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtg 510 :::: :::: d1jmva_ 132 dMLVV-PLRD-------------------------------------------------- 140 query 511 adaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1jmva_ 141 ---------------------------------------------------------- 141 FAST alignment (Normalized score: 3.30 Raw score:930.50) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1jmva_ 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1jmva_ 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1jmva_ 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1jmva_ 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1jmva_ 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQ------NV 354 ::::::::::::::::::::::::: :: d1jmva_ 1 -----------------------MYKHILVAVDLSEESPILLKKAVGI----AKRHDAKL 33 query 355 YGVSMPSKYSS-----------------------DHSKGDAAELAR--RTGL-NFRTVSI 388 :::::: :::::::::::: :::: ::::: d1jmva_ 34 SIIHVD-----VNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSG-- 86 query 389 EPMFDAYMASLGLTGLAEENLQSR--LRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTL 445 :::::::::::::: :::::::: d1jmva_ 87 ------------------------SGDLGQVLSDAIEQYDVDLLVTGHH----------- 111 query 446 Y-------------GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKP 492 :::::: d1jmva_ 112 -QDFWSKLMSSTRQVMNTIK---------------------------------------- 130 query 493 DYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGF 552 d1jmva_ 131 ------------------------------------------------------------ 131 query 553 GKDRRLPITNRWREGH---------- 568 d1jmva_ 131 ----------------IDMLVVPLRD 140 TMalign alignment (TM-score: 0.17 Raw score:95.23) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1jmva_ 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1jmva_ 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1jmva_ 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1jmva_ 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1jmva_ 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALG--AQNVYGVS 358 ::::::::::::::::::::::::::: :::::::: d1jmva_ 1 -----------------------MYKHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIH 37 query 359 MPSK---------------------YSSDHSKGDAAELARRT--GLNFRTVSIEPMFDAY 395 :::: :: :::::::::::: ::::::::: d1jmva_ 38 VDVNFSDLYTGLIDVNMSSMQDRIS--TE-TQKALLDLAESVDYPISEKLSGS------- 87 query 396 MASLGLTGLAEENLQSRLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG-- 451 : ::::::::::::::: ::::::: ::::::::: ::: :: d1jmva_ 88 --------------G--DLGQVLSDAIEQYDVDLLVTGHH-QDFWSKLMS--STRQVMNT 128 query 452 ----AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDR 507 ::: :: : :: d1jmva_ 129 IKIDMLV-VP-L-RD--------------------------------------------- 140 query 508 DTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREG 567 d1jmva_ 141 ------------------------------------------------------------ 141 query 568 H 568 d1jmva_ 141 - 141 HHsearch alignment (Probability: 0.04 E-value:0.35) query 19 AGNAEAILRWTRHSAEQGAHLVAF------PEMALTGYPVEDLALRSSFVEASRTALREL 72 :::::::::::::::::::::::: :::::::::::::::::::::::::::::: d1jmva_ 13 EESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDL 72 query 73 AAR 75 ::: d1jmva_ 73 AES 75
Intermediate <-- 0.943 --> Hit
DALI alignment (Z-score: 4.9 Raw score:388.10) d1jmva_ 1 ----MYKHILVAVDLSEESPILLKKAVGIAKRHdAKLSIIHVDvnfsdlytglidvnmss 56 ::::::::::::::::::::::::::::: ::::::::: d1p3y1_ 1 isilKDKKLLIGICGSISSVGISSYLLYFKSFF-KEIRVVMTK----------------- 42 d1jmva_ 57 mqdristetqkALLDLAEsvdypISEKLSGSG--dlgqVLSDAIEqyDVDLLVTG-HHQD 113 ::::::: ::::::::: ::::::: :::::::: :::: d1p3y1_ 43 -----taedliPAHTVSY----fCDHVYSEHGengkrhSHVEIGR--WADIYCIIpATAN 91 d1jmva_ 114 fwSKLMSS-----trQVMNTIKIDMLVVPLRD---------------------------- 140 :::::: ::::::::::::::::: d1p3y1_ 92 ilGQTANGvamnlvaTTVLAHPHNTIFFPNMNdlmwnktvvsrnieqlrkdghiviepve 151 d1jmva_ 141 -------------------- 141 d1p3y1_ 152 imrglitpdkallaiekgfk 171 FAST alignment (Normalized score: 3.60 Raw score:556.50) d1jmva_ 1 MY------KHILVAVDLSE---ESPILLKKAVGIAKRHD--AKLSIIHVDVNFSDLYTGL 49 ::::::::::: ::::::::::: :::::::: d1p3y1_ 1 --ISILKDKKLLIGICGSISSVGISSYLLYFKS------FFKEIRVVMT----------- 41 d1jmva_ 50 IDVNMSSMQDRISTETQK-------ALLDLAESVDYP-ISEKLSGSGDLG---------- 91 ::::::: :::::: d1p3y1_ 42 ------------------KTAEDLIPAHTVSY-----FCDHVYS------EHGENGKRHS 72 d1jmva_ 92 ------------------------------QVLSDAIEQYDV---DLLVTGHHQ---DFW 115 :::::::::: :::::::: ::: d1p3y1_ 73 HVEIGRWADIYCIIPATANILGQTANGVAMNLVATTVLAH--PHNTIFFPNMN-DLMWNK 129 d1jmva_ 116 SKLMSSTRQVMNTIKIDMLVVPLRD----------------------- 140 :::::::::::: ::::::: d1p3y1_ 130 TVVSRNIEQLRK-DGHIVIE-----PVEIMRGLITPDKALLAIEKGFK 171 TMalign alignment (TM-score: 0.49 Raw score:68.82) d1jmva_ 1 ---M--YKHILVAVDLSEESPILLKKAV-GIAKRHDAKLSIIHVDVNFSDLYTGLIDVNM 54 : ::::::::: :::::: ::::: :::::::::::::: d1p3y1_ 1 ISILKDKKLLIGICG-SISSVG-ISSYLLYFKSFFKEIRVVMT----------------- 41 d1jmva_ 55 SSMQDRISTETQKALLDLAESV--DYPISEKLS--------------------------G 86 :::::::: :::: ::::::::: d1p3y1_ 42 ---------KTAEDLIP-AHTVSYFCDHVYSEHGENGKRHSHVEIGRWADIYCIIPATA- 90 d1jmva_ 87 SG-DLG---QV---LSDAIEQYDVDLLVTGHHQDF-WSK--LMSSTRQVMNTIKIDMLVV 136 :: ::: :: ::::::::::::::::::::: ::: ::::::::::: ::::::: d1p3y1_ 91 NILGQTANGVAMNLVATTVLAHPHNTIFFPNMNDLMWNKTVVSRNIEQLRKD-GHIVIEP 149 d1jmva_ 137 -----PLR--------------D 140 ::: d1p3y1_ 150 VEIMRGLITPDKALLAIEKGFK- 171 HHsearch alignment (Probability: 0.42 E-value:0.00) d1jmva_ 2 YKHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIHVDV 40 ::::::::::::::::::::::: ::::::::::::::: d1p3y1_ 6 DKKLLIGICGSISSVGISSYLLY-FKSFFKEIRVVMTKT 43