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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1jmva_ | Universal stress protein A, UspA | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1gtra2 | Glutaminyl-tRNA synthetase (GlnRS) | Nucleotidylyl transferase | Adenine nucleotide alpha hydrolase-like | α/β |
Query <-- 0.827 --> IntermediateDALI 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 <-- 0.622 --> HitDALI alignment (Z-score: 7.3 Raw score:619.10) d1jmva_ 1 -----------------MYKHILVAVD----LSEESPILLKKAVGIAKRHDAKLSIIHVD 39 :::::::::: ::::::::::::::::::::::::::::: d1gtra2 1 tnfirqiidedlasgkhTTVHTRFPPEpngyLHIGHAKSICLNFGIAQDYKGQCNLRFDD 60 d1jmva_ 40 VNfsdlytglidvnmssmqdriSTETQKALLDLAESVDYPIS-EKLSGS----------- 87 :: :::::::::::::::::::: :::::: d1gtra2 61 TN----------------pvkeDIEYVESIKNDVEWLGFHWSgNVRYSSdyfdqlhayai 104 d1jmva_ 88 ------------------------------------------------------------ 88 d1gtra2 105 elinkglayvdeltpeqireyrgtltqpgknspyrdrsveenlalfekmraggfeegkac 164 d1jmva_ 88 -------------------------------------GDLGQVLSDAIEQYDVDLLVTGH 110 ::::::::::::::::::::::: d1gtra2 165 lrakidmaspfivmrdpvlyrikfaehhqtgnkwciyPMYDFTHCISDALEGITHSLCTL 224 d1jmva_ 111 hqdfwskLMSSTRQVMNTI-------KIDMLVVPLRD----------------------- 140 :::::::::::: ::::::::::: d1gtra2 225 ------eFQDNRRLYDWVLdnitipvHPRQYEFSRLNleytvmskrklnllvtdkhvegw 278 d1jmva_ 141 ----------------------------------------------------- 141 d1gtra2 279 ddprmptisglrrrgytaasirefckrigvtkqdntiemaslesciredlnen 331 FAST alignment (Normalized score: 5.80 Raw score:1249.00) d1jmva_ 1 MY-------------------KHILVAVD----LSEESPILLKKAVGIAKRHDAKLSIIH 37 :::::::: ::::::::::::::::::::::::::: d1gtra2 1 --TNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLRF 58 d1jmva_ 38 VDVNFSDLYTGLIDVNMSSMQDRIS-------TETQKALLDLAESVDYP-ISEKLSG--- 86 :: ::::::::::::::::: :::::: d1gtra2 59 DD-----------------------TNPVKEDIEYVESIKNDVEWLGFHWSGNVRY-SSD 94 d1jmva_ 87 ------------------------------------------------------------ 87 d1gtra2 95 YFDQLHAYAIELINKGLAYVDELTPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMR 154 d1jmva_ 87 ----------------------------------------------SGDLGQVLSDAIEQ 100 :::::::::::::: d1gtra2 155 AGGFEEGKACLRAKIDMASPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDAL 214 d1jmva_ 101 YDVDLLVTGHHQDFW-SKLMSSTRQVMNTI--------KIDMLVVPLRD----------- 140 :::::::: ::::::::::::: :::::::: d1gtra2 215 EGITHSLC-------TLEFQDNRRLYDWV-LDNITIPVHPRQYEFS---RLNLEYTVMSK 263 d1jmva_ 141 ------------------------------------------------------------ 141 d1gtra2 264 RKLNLLVTDKHVEGWDDPRMPTISGLRRRGYTAASIREFCKRIGVTKQDNTIEMASLESC 323 d1jmva_ 141 -------- 141 d1gtra2 324 IREDLNEN 331 TMalign alignment (TM-score: 0.63 Raw score:87.88) d1jmva_ 1 -----------------MYKHILVAVD---LSE-ESPILLKKAVGIAKRHDAKLSIIHVD 39 :::::::::: ::: :::::::::::::::::::::::::: d1gtra2 1 TNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLRFDD 60 d1jmva_ 40 VNF---SDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPIS-EKLSGS-------- 87 ::: :::::::::::::::::::: :::::: d1gtra2 61 TNPVKE-------------------DIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHA 101 d1jmva_ 88 ------------------------------------------------------------ 88 d1gtra2 102 YAIELINKGLAYVDELTPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEG 161 d1jmva_ 88 ----------------------------------------GDLGQVLSDAIEQYDVDLLV 107 :::::::::::::::::::: d1gtra2 162 KACLRAKIDMASPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSL 221 d1jmva_ 108 TGHHQDFWSKLMSSTRQVMNTI-------KIDMLVVPLRD-------------------- 140 ::: : :::::::::::: ::::::::::: d1gtra2 222 CTL--E----FQDNRRLYDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHV 275 d1jmva_ 141 -------------------------------------------------------- 141 d1gtra2 276 EGWDDPRMPTISGLRRRGYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNEN 331 HHsearch alignment (Probability: 0.01 E-value:0.97) d1jmva_ 20 KKAVGIAKRHDAKLS 34 ::::::::::::::: d1gtra2 41 CLNFGIAQDYKGQCN 55