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 | d1u3da2 | Cryptochrome | Cryptochrome/photolyase, N-terminal domain | Cryptochrome/photolyase, N-terminal 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 <-- 1.725 --> HitDALI alignment (Z-score: 9.3 Raw score:625.90) d1jmva_ 1 mykHILVAVD--LSEEsPILLKKAVGIAkrhdaKLSIIHVDVNFSdlytglidvnmssmq 58 ::::::: :::: ::::::::::: :::::::::::: d1u3da2 1 ---CSIVWFRrdLRVEdNPALAAAVRAG-----PVIALFVWAPEE--------eghyhpg 44 d1jmva_ 59 driSTETQKALLDLAESV--DYPIseKLSGSG-DLGQVLSDAIEQYDVDLLVTGHHQdfW 115 ::::::::::::::: :::: :::::: :::::::::::::::::::::::: : d1u3da2 45 rvsRWWLKNSLAQLDSSLrsLGTC--LITKRStDSVASLLDVVKSTGASQIFFNHLY--D 100 d1jmva_ 116 SKLMSSTRQVMNTI---KIDMLVVPLRD-------------------------------- 140 :::::::::::::: ::::::::::: d1u3da2 101 PLSLVRDHRAKDVLtaqGIAVRSFNADLlyepwevtdelgrpfsmfaafwerclsmpydp 160 d1jmva_ 141 ------------------------- 141 d1u3da2 161 espllppkkiisgdvskcvadplvf 185 FAST alignment (Normalized score: 7.24 Raw score:1165.00) d1jmva_ 1 MYKHILVAVDLSEES--------PILLKKAVGIAKRHD-AKLSIIHVDVNFSDLYTGLID 51 :::::: ::::::::: ::::::::::: d1u3da2 1 ---CSIVWF------RRDLRVEDNPALAAAVR------AGPVIALFVWAP---------- 35 d1jmva_ 52 VNMSSMQDRIS----------------TETQKALLDLAESVDYPISEKLSG-SGDLGQVL 94 :::::::::::: ::: :::::: :::::::: d1u3da2 36 -----------EEEGHYHPGRVSRWWLKNSLAQLDSSLR--SLG-TCLITKRSTDSVASL 81 d1jmva_ 95 SDAIEQYDVDLLVTGHHQDFWSKLMSSTRQVMNT---IKIDMLVVPLRD----------- 140 :::::::::::::::::: :::::::::::::: :::::::::: d1u3da2 82 LDVVKSTGASQIFFNHLY--DPLSLVRDHRAKDVLTAQGIAVRSFNA--DLLYEPWEVTD 137 d1jmva_ 141 ------------------------------------------------ 141 d1u3da2 138 ELGRPFSMFAAFWERCLSMPYDPESPLLPPKKIISGDVSKCVADPLVF 185 TMalign alignment (TM-score: 0.60 Raw score:84.25) d1jmva_ 1 MYKHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIHVDVNFS----------DLYTGLI 50 ::::::: : :::::::::::::::: ::::::::::::: d1u3da2 1 ---CSIVWFR-R-DLRVEDNPALAAAVRA-GPVIALFVWAPEEEGHYHPGRVS------- 47 d1jmva_ 51 DVNMSSMQDRISTE-TQKALLDLAESV-DYPISEKLSGSGDLGQVLSDAIEQYDVDLLVT 108 :: :::::::::::: :::::::::::::::::::::::::::::::: d1u3da2 48 ------------RWWLKNSLAQLDSSLRSLGTCLITKRSTDSVASLLDVVKSTGASQIFF 95 d1jmva_ 109 GHHQDFWSKLMSSTRQVMNTI---KIDMLVVPLRD------------------------- 140 :::::: ::: :::::::::: ::::::::::: d1u3da2 96 NHLYDP-LSL-VRDHRAKDVLTAQGIAVRSFNADLLYEPWEVTDELGRPFSMFAAFWERC 153 d1jmva_ 141 -------------------------------- 141 d1u3da2 154 LSMPYDPESPLLPPKKIISGDVSKCVADPLVF 185 HHsearch alignment (Probability: 0.83 E-value:0.00) d1jmva_ 13 EESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDL 72 ::::::::::: :::::::::::::::::::::: ::::::::::::::::: d1u3da2 12 VEDNPALAAAV-----RAGPVIALFVWAPEEEGHYHPG-----RVSRWWLKNSLAQLDSS 61 d1jmva_ 73 AESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQDFWS-KLMSSTRQVMNTIKI 131 :::::::: :::::::::::::::::::::::::::::::::: ::::::::::::::: d1u3da2 62 LRSLGTCL--ITKRSTDSVASLLDVVKSTGASQIFFNHLYDPLSLVRDHRAKDVLTAQGI 119 d1jmva_ 132 DMLVV 136 ::::: d1u3da2 120 AVRSF 124