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 | d1ps9a3 | 2,4-dienoyl-CoA reductase, middle domain | Nucleotide-binding domain | Nucleotide-binding domain | 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 <-- 0.920 --> HitDALI alignment (Z-score: 3.8 Raw score:349.30) d1jmva_ 1 -----------------------------------------MYKHILVAVdlseeSPILL 19 ::::::::: ::::: d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavQKKNLAVVG----aGPAGL 56 d1jmva_ 20 KKAVGIAKRhDAKLSIIHVdvnfsdlytglidvnmssmqdristetQKAL---------- 69 ::::::::: ::::::::: :::: d1ps9a3 57 AFAINAAAR-GHQVTLFDA---------------------------HSEIggqfniakqi 88 d1jmva_ 70 ----------ldLAESV-DYPISEKLSGsgdLGQVLSdaieqyDVDLLVTG-HHQDfwsk 117 ::::: :::::::::: :::::: :::::::: :::: d1ps9a3 89 pgkeefyetlryYRRMIeVTGVTLKLNH-tvTADQLQ------AFDETILAsGIPN---- 137 d1jmva_ 118 lmsSTRQVMNTiKIDMLVVPL---------------------rd 140 :::::::: ::::::::: d1ps9a3 138 -raLAQPLIDS-GKTVHLIGGcdvameldarraiaqgtrlalei 179 FAST alignment (Normalized score: 3.46 Raw score:547.60) d1jmva_ 1 MY-------------------------------------------KHILVAVDLSEE--- 14 ::::: d1ps9a3 1 --INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAV-------VGA 51 d1jmva_ 15 SPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRIS------------ 62 ::::::::::::: ::::::::: d1ps9a3 52 GPAGLAFAINAAA-RGHQVTLFD-------------------------AHSEIGGQFNIA 85 d1jmva_ 63 ---------TETQKALLDLAESVDYPISEKLSGSGD--------LGQVLSDAIEQ-YDVD 104 :::::::::::: :::: :::: :::: d1ps9a3 86 KQIPGKEEFYETLRYYRRMIE--VTGV---------TLKLNHTVTADQ-------LQAFD 127 d1jmva_ 105 LLVTGHHQDFWSK--LMSSTRQVMNTIKIDMLVVPLRD---------------------- 140 ::::::: :::::::::: :::::::: d1ps9a3 128 ETILASG------IPNRALAQPLID-SGKTVHLI----GGCDVAMELDARRAIAQGTRLA 176 d1jmva_ 141 --- 141 d1ps9a3 177 LEI 179 TMalign alignment (TM-score: 0.50 Raw score:69.40) d1jmva_ 1 -----------------------------------------MYKHILVAVDLSEESPILL 19 ::::::::: : ::::: d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG-A---GPAGL 56 d1jmva_ 20 KKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALL--------- 70 ::::::::: ::::::::: : :::: d1ps9a3 57 AFAINAAAR-GHQVTLFDA--------------------------H-SEIGGQFNIAKQI 88 d1jmva_ 71 ---------DLAESVD---YPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQDFWSKL 118 ::::::: ::::::::::: :::: ::: ::::::::::: :: d1ps9a3 89 PGKEEFYETLRYYRRMIEVTGVTLKLNHTV-TADQ---LQA---FDETILASGIP---NR 138 d1jmva_ 119 MSSTRQVMNTIKIDMLVVPL------RD--------------- 140 ::::::::: ::::::::: :: d1ps9a3 139 -ALAQPLIDS-GKTVHLIGGCDVAMELDARRAIAQGTRLALEI 179 HHsearch alignment (Probability: 0.04 E-value:0.17) d1jmva_ 18 LLKKAVGIAKRHDAKLSIIHVDVNFSDLYTG-LIDVNMSSMQDRISTETQKALLDLAESV 76 :::::::: :::::::::::::::::::::: :::::: ::::::::::::::::: d1ps9a3 55 GLAFAINA-AARGHQVTLFDAHSEIGGQFNIAKQIPGK-----EEFYETLRYYRRMIEVT 108 d1jmva_ 77 DYPISEKLSGSGDLGQVLSDAIEQYDVDLLV--TGHHQDFW 115 :::::::::::::: : ::::::: :::::::: d1ps9a3 109 GVTLKLNHTVTADQ-------L--QAFDETILASGIPNRAL 140