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 | d1gcaa_ | Galactose/glucose-binding protein | Periplasmic binding protein-like I | Periplasmic binding protein-like I | 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 <-- 0.885 --> HitDALI alignment (Z-score: 4.8 Raw score:373.10) d1jmva_ 1 MYKHILVAV-DLSE-ESPILLKKAVGIAKRH-DAKLSIIHVDVNfsdlytglidvnmssm 57 ::::::::: :::: :::::::::::::::: :::::::::::: d1gcaa_ 1 ADTRIGVTIyKYDDnFMSVVRKAIEKDGKSApDVQLLMNDSQND---------------- 44 d1jmva_ 58 qdristetqkalldlaesvdypiseklsgsGDLGQVLSDAIEqYDVDLLVTGhhqdfwsk 117 :::::::::::: ::::::::: d1gcaa_ 45 -----------------------------qSKQNDQIDVLLA-KGVKALAIN------lv 68 d1jmva_ 118 LMSSTRQVMNTI---KIDMLVVP------------------------------------- 137 :::::::::::: :::::::: d1gcaa_ 69 DPAAAGTVIEKArgqNVPVVFFNkepsrkaldsydkayyvgtdskesgviqgdliakhwq 128 d1jmva_ 138 ------------------------------------------------------------ 138 d1gcaa_ 129 anqgwdlnkdgkiqyvllkgepghpdaearttyvvkelndkgiqteqlaldtamwdtaqa 188 d1jmva_ 138 ------------------------------------------------------------ 138 d1gcaa_ 189 kdkmdawlsgpnankievvianndamamgavealkahnkssipvfgvdalpealalvksg 248 d1jmva_ 138 ----------------------------------------------------------lr 139 d1gcaa_ 249 amagtvlndannqakatfdlaknlaegkgaadgtswkienkivrvpyvgvdkdnlseftq 308 d1jmva_ 140 d 140 d1gcaa_ 309 k 309 FAST alignment (Normalized score: 2.23 Raw score:464.60) d1jmva_ 1 MYKHILVAVDLSE----------------------------------------------- 13 d1gcaa_ 1 -------------ADTRIGVTIYKYDDNFMSVVRKAIEKDGKSAPDVQLLMNDSQNDQSK 47 d1jmva_ 14 ------------------------------------------------------------ 14 d1gcaa_ 48 QNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYY 107 d1jmva_ 14 ---ESPILLKKAVGIAKRH--------------DAKLSIIHVDVNFSDLYTGLIDVNMSS 56 ::::::::::::::: :::::::: d1gcaa_ 108 VGTDSKESGVIQGDLIAK-HWQANQGWDLNKDGKIQYVLLK------------------- 147 d1jmva_ 57 MQDR--ISTETQKALLDLAESV-------DYPISEKLSGSGD------------------ 89 ::::::::::::::: :::::::::: d1gcaa_ 148 ----GEPGHPDAEARTTYVVK-ELNDKGIQTEQLALDTA---MWDTAQAKDKMDAWLSGP 199 d1jmva_ 90 -----------LGQVLSDAIEQYDV--------DLLVTGHHQDFWSKLMSS---TRQVMN 127 ::::::::::: ::::: :::::: d1gcaa_ 200 NANKIEVVIANNDAMAMGAVEA---LKAHNKSSIPVFG-------------VDALPEALA 243 d1jmva_ 128 TIKID-------MLVVPLRD---------------------------------------- 140 :::::: d1gcaa_ 244 -----LVKSGAMAGTVLN--DANNQAKATFDLAKNLAEGKGAADGTSWKIENKIVRVPYV 296 d1jmva_ 141 ------------- 141 d1gcaa_ 297 GVDKDNLSEFTQK 309 TMalign alignment (TM-score: 0.47 Raw score:65.90) d1jmva_ 1 MYKHILVAV-DL-SE-ESPILLKKAVGIAKRHDAKLSIIHVD-VNFSDLYTGLIDVNMSS 56 ::::::::: :: :: :::::::::::::::::::::::::: :: d1gcaa_ 1 ADTRIGVTIYKYDDNFMSVVRKAIEKDGKSAPDVQLLMNDSQNDQ--------------- 45 d1jmva_ 57 MQDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQDFWS 116 :::: ::::::::::::::::::: d1gcaa_ 46 -------------------------------SKQN-DQIDVLLAKGVKALAINLV----- 68 d1jmva_ 117 KLMSSTRQVMNTI--K-IDMLVVP-----------------L------------------ 138 :: :::::::::: : ::::::: : d1gcaa_ 69 DP-AAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGVIQGDLIAKHW 127 d1jmva_ 139 ------------------------------------------------------------ 139 d1gcaa_ 128 QANQGWDLNKDGKIQYVLLKGEPGHPDAEARTTYVVKELNDKGIQTEQLALDTAMWDTAQ 187 d1jmva_ 139 -----------------------------------------------RD----------- 140 :: d1gcaa_ 188 AKDKMDAWLSGPNANKIEVVIANNDAMAMGAVEALKAHNKSSIPVFGVDALPEALALVKS 247 d1jmva_ 141 ------------------------------------------------------------ 141 d1gcaa_ 248 GAMAGTVLNDANNQAKATFDLAKNLAEGKGAADGTSWKIENKIVRVPYVGVDKDNLSEFT 307 d1jmva_ 141 -- 141 d1gcaa_ 308 QK 309 HHsearch alignment (Probability: 0.17 E-value:0.16) d1jmva_ 90 LGQVLSDAIEQYDV-DLLVTG 109 :::::::::::::: :::::: d1gcaa_ 214 MAMGAVEALKAHNKSSIPVFG 234