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 <-- 0.839 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1nhpa1) 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 d1nhpa1 NADH peroxidaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/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 <-- 0.839 --> Hit
DALI alignment (Z-score: 3.4 Raw score:353.90) d1jmva_ 1 myKHILVAVdlseeSPILLKKAVGIAKRH-DAKLSIIHVdvnfsdlytglidvnmssmqd 59 ::::::: ::::::::::::::: ::::::::: d1nhpa1 1 --MKVIVLG----sSHGGYEAVEELLNLHpDAEIQWYEK--------------------- 33 d1jmva_ 60 ristetQKAL----------------------lDLAESV-dYPISeKLSG-sgDLGQ--- 92 :::: :::::: :::: :::: :::: d1nhpa1 34 ------GDFIsflsagmqlylegkvkdvnsvryMTGEKMesRGVN-VFSNteiTAIQpke 86 d1jmva_ 93 -------vlsdaiEQYDVDLLVTGHHQDF-----wskLMSSTRQVMN------------- 127 :::::::::::::::: :::::::::: d1nhpa1 87 hqvtvkdlvsgeeRVENYDKLIISPGAVPfeldgvrpNTAWLKGTLElhpngliktdeym 146 d1jmva_ 128 -tiKIDMLVVPL--------------------------------------rd 140 ::::::::: d1nhpa1 147 rtsEPDVFAVGDatlikynpadtevnialatnarkqgrfavknleepvkpfp 198 FAST alignment (Normalized score: 2.62 Raw score:436.80) d1jmva_ 1 MYKHILVAVDLSEE---SPILLKKAVGIAKR-HDAKLSIIHVDVNFSDLYTGLIDVNMSS 56 ::::: :::::::::::::: ::::::::: d1nhpa1 1 --MKVIV-------LGSSHGGYEAVEELLNLHPDAEIQWYE------------------- 32 d1jmva_ 57 MQDRISTETQKALLD-----------------------------LAES-VDYPISEKLSG 86 :::: :::: :::: d1nhpa1 33 ---------------KGDFISFLSAGMQLYLEGKVKDVNSVRYMTGEKMESRG-VNVF-- 74 d1jmva_ 87 SGDLGQVLSDAIE--------------------------QYDVDLLVTGHHQDFWS---- 116 :::::::::::::: d1nhpa1 75 -------------SNTEITAIQPKEHQVTVKDLVSGEERVENYDKLIISPGAV---PFEL 118 d1jmva_ 117 ----KLMSSTRQVMNTIKI--------------------DMLVVPLRD------------ 140 ::::::::: :::: d1nhpa1 119 DGVRPNTAWLKGT------LELHPNGLIKTDEYMRTSEPDVFA-----VGDATLIKYNPA 167 d1jmva_ 141 ------------------------------- 141 d1nhpa1 168 DTEVNIALATNARKQGRFAVKNLEEPVKPFP 198 TMalign alignment (TM-score: 0.48 Raw score:67.51) d1jmva_ 1 MYKHILVAVDLSEESPILLKKAVGIAKRH-DAKLSIIHVDVNFSDLYTGLIDVNMSSMQD 59 ::::::: : ::::::::::::::: ::::::::: d1nhpa1 1 --MKVIVLG-S---SHGGYEAVEELLNLHPDAEIQWYEK--------------------- 33 d1jmva_ 60 RISTETQKALL----------------------DLAESV-DYPISEKLSGSGDLGQV--- 93 :: ::: :::::: ::::::::::: ::::: d1nhpa1 34 -----GD-FISFLSAGMQLYLEGKVKDVNSVRYMTGEKMESRGVNVFSNTE-ITAIQPKE 86 d1jmva_ 94 -LSDA--------IEQYDVDLLVTG-HH-------QDF-----------WS-KLMS---- 120 :::: ::: :::::::: :: ::: :: :::: d1nhpa1 87 HQVTVKDLVSGEERVE-NYDKLIISPGAVPFELDGVRPNTAWLKGTLELHPNGLIKTDEY 145 d1jmva_ 121 --STRQVMNTIKIDMLVVPL----------------RD---------------------- 140 :: ::::::::: :: d1nhpa1 146 MR-----TS--EPDVFAVGDATLIKYNPADTEVNIALATNARKQGRFAVKNLEEPVKPFP 198 HHsearch alignment (Probability: 0.09 E-value:0.01) d1jmva_ 15 SPILLKKAVGIAKR-HDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDLA 73 :::::::::::::: :::::::::::::::::::::::::::::: ::::::::::::: d1nhpa1 9 SHGGYEAVEELLNLHPDAEIQWYEKGDFISFLSAGMQLYLEGKVK--DVNSVRYMTGEKM 66 d1jmva_ 74 ESVDYPISEKLSGSG------D--LGQVLSDAIEQYDVDLLVTGHH 111 ::::::::::::::: : :::::::::::::::::::::: d1nhpa1 67 ESRGVNVFSNTEITAIQPKEHQVTVKDLVSGEERVENYDKLIISPG 112