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 | d6ldha1 | Lactate dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 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 <-- 1.421 --> HitDALI alignment (Z-score: 5.6 Raw score:433.10) d1jmva_ 1 ------------------myKHILVAVdlseeSPILLKKAVGIAKRHDA-KLSIIHVdvn 41 ::::::: ::::::::::::::::: ::::::: d6ldha1 1 atlkdklighlatsqeprsyNKITVVG----vGAVGMACAISILMKDLAdEVALVDV--- 53 d1jmva_ 42 fsdlytglidvnmssmqdristeTQKALLDLAESVD-------ypiSEKLSGsgdlgqvl 94 ::::::::::::: :::::: d6ldha1 54 -----------------------MEDKLKGEMMDLQhgslflhtakIVSGKD-------- 82 d1jmva_ 95 SDAIEqyDVDLLVTG-HHQD--------FWSKLMSSTRQVMNTIK-----IDMLVVP--- 137 ::::: :::::::: :::: ::::::::::::::::: ::::::: d6ldha1 83 YSVSA--GSKLVVITaGARQqegesrlnLVQRNVNIFKFIIPNIVkhspdCIILVVSnpv 140 d1jmva_ 138 -----------------lrd 140 d6ldha1 141 dvltyvawklsglpmhriig 160 FAST alignment (Normalized score: 4.80 Raw score:718.30) d1jmva_ 1 MY--------------------KHILVAVDLSEESPILLKKAVGIAKRHDAK----LSII 36 ::::: ::::: ::::::::::: :::: d6ldha1 1 --ATLKDKLIGHLATSQEPRSYNKITV-VGVGA---VGMACAISILM-----KDLADEVA 49 d1jmva_ 37 HVDVNFSDLYTGLIDVNMSSMQDRIS----TETQKALLDLAES-VDYPISEKLSGSGDLG 91 :: ::::::::::::: :::::::::::: :: d6ldha1 50 LV------------------------DVMEDKLKGEMMDLQHGSLFLHTAKIVSGK--DY 83 d1jmva_ 92 QVLSDAIEQ-YDVDLLVTGHHQD-------------FWSKLMSSTRQVMNT-----IKID 132 :: ::::::::: ::::::::::::::: :::: d6ldha1 84 SV-------SAGSKLVVIT----AGARQQEGESRLNLVQRNVNIFKFIIPNIVKHSPDCI 132 d1jmva_ 133 MLVVPLRD------------------------- 140 ::: d6ldha1 133 ILV-----VSNPVDVLTYVAWKLSGLPMHRIIG 160 TMalign alignment (TM-score: 0.51 Raw score:71.84) d1jmva_ 1 -------------------MYKHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIHVDVN 41 :::::::: ::::::::::::::: :: ::::::::: d6ldha1 1 ATLKDKLIGHLATSQEPRS-YNKITVVG-VGAVGMACAISILMK-DL-ADEVALVDV--- 53 d1jmva_ 42 FSDLYTGLIDVNMSSMQDRISTETQKALLDLAESV--D-----Y-PISEKLSG------- 86 :::::::::::: : : :::::::: d6ldha1 54 -----------------------MEDKLKGEMMDLQHGSLFLHTAKIVSGKDYSVSAGSK 90 d1jmva_ 87 ------------------------SGDLGQVLSDAIEQYDVDLLVTGHHQDFWSKLMSST 122 ::::::::::::::::::::::: : :::::: d6ldha1 91 LVVITAGARQQEGESRLNLVQRNV-NIFKFIIPNIVKHSPDCIILVVS--N---PVDVLT 144 d1jmva_ 123 RQVMNTI-KI--DMLVVPLRD 140 ::::::: :: :::: d6ldha1 145 YVAWKLSGLPMHRIIG----- 160 HHsearch alignment (Probability: 0.03 E-value:0.08) d1jmva_ 119 MSSTRQVMNTIKIDMLVV 136 :::::::::::::::::: d6ldha1 118 KFIIPNIVKHSPDCIILV 135