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 | d1jkea_ | D-Tyr tRNAtyr deacylase, DTD | DTD-like (Pfam 02580) | DTD-like (Pfam 02580) | 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 <-- 1.003 --> HitDALI alignment (Z-score: 3.9 Raw score:324.60) d1jmva_ 1 ----------------------myKHILVAVDL-----sEESPILLKKAVG--------- 24 ::::::::: :::::::::::: d1jkea_ 1 mialiqrvtrasvtvegevtgeigAGLLVLLGVekdddeQKANRLCERVLGyrifsdaeg 60 d1jmva_ 25 ----IAKRHDAKLSIIHVDV--NFSDlytglidvnmssmqdriSTETQKALLDLAESVD- 77 :::::::::::::::: :::: :::::::::::::::: d1jkea_ 61 kmnlNVQQAGGSVLVVSQFTlaADTE-----rgmrpsfskgasPDRAEALYDYFVERCRq 115 d1jmva_ 78 --YPISEKLSGsgdlgqvlsDAIEqydvdllvtghhqdfwsklmsstrqvmntikIDMLV 135 ::::::::: :::: ::::: d1jkea_ 116 qeMNTQTGRFA------admQVSL---------------------------vndgPVTFW 142 d1jmva_ 136 VPLrd 140 ::: d1jkea_ 143 LQV-- 145 FAST alignment (Normalized score: 2.64 Raw score:376.50) d1jmva_ 1 MY------------------------KHILVAVDLSEE-SPILLKKAVGIAK-------- 27 :::::::::::: ::::::::::::: d1jkea_ 1 --MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDA 58 d1jmva_ 28 ---------RHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRIS---------------- 62 ::::::::::: d1jkea_ 59 EGKMNLNVQQAGGSVLVVSQ------------------------FTLAADTERGMRPSFS 94 d1jmva_ 63 -----TETQKALLDLAES-VDYPISEKLS------GSGDLGQVLSDAIEQYDVDLLVTGH 110 ::::::::::::: ::::: :::: d1jkea_ 95 KGASPDRAEALYDYFVERCRQQEM-----NTQTGRFAAD--------------------- 128 d1jmva_ 111 HQDFWSKLMSSTRQVMNTIK---------IDMLVVPLRD-- 140 :::::: d1jkea_ 129 --------------------MQVSLVNDGPVTFWL----QV 145 TMalign alignment (TM-score: 0.45 Raw score:62.82) d1jmva_ 1 ------MY----------------KHILVAVDL---SE--ESPILLKKAVG--------- 24 :: ::::::::: :: ::::::::::: d1jkea_ 1 MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAEG 60 d1jmva_ 25 ----IAKRHDAKLSIIHVDV--N------FS-------DLYTGLIDVNMSSMQDRISTE- 64 :::::::::::::::: : :: :: d1jkea_ 61 KMNLNVQQAGGSVLVVSQFTLAADTERGMRPSFSKGAS-------------------PDR 101 d1jmva_ 65 TQKALLDLAESV--DYPISEKL-SGSGDLGQVLSDAIEQYDVDLLVTGHHQDFWSKLMSS 121 :::::::::::: :::::::: :::: : :: : :::: d1jkea_ 102 AEALYDYFVERCRQQEMNTQTGRFAAD----M--QV-S--LVND---------------- 136 d1jmva_ 122 TRQVMNTIKIDMLVVPLRD 140 ::::::::: d1jkea_ 137 --------GPVTFWLQV-- 145 HHsearch alignment (Probability: 0.01 E-value:0.39) d1jmva_ 31 AKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISE 82 :::::::::::::::::::::::::::::::::::::::::::::::::::: d1jkea_ 71 GSVLVVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVERCRQQEMNTQT 122