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 | d1j31a_ | Hypothetical protein PH0642 | Carbon-nitrogen hydrolase | Carbon-nitrogen hydrolase | α+β |
| Hit | d1f89a_ | hypothetical protein yl85 | Carbon-nitrogen hydrolase | Carbon-nitrogen hydrolase | α+β |
Query <-- 1.000 --> IntermediateDALI alignment (Z-score: 28.1 Raw score:2714.30) query 1 slQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVED--LALR 58 :::::::::::::::::::::::::::::::::::::::::::::::::::: :::: d1j31a_ 1 --MVKVGYIQMEPKILELDKNYSKAEKLIKEASKEGAKLVVLPELFDTGYNFESreEVFD 58 query 59 ssFVEA--sRTALRELAARLAeegFGELPVLVGYLDRSEsaqpkygqpaGAPRNAAAVLH 116 :::: :::::::::::: ::::::::::::::: ::::::::::: d1j31a_ 59 --VAQQipeGETTTFLMELAR---ELGLYIVAGTAEKSG----------NYLYNSAVVVG 103 query 117 RGRVALTFAKHHLPnygvFDEFRYFVPGD-TMPIVRLHGVDIALAICEDLWQDgGRVPAA 175 :::::::::::::: ::::::::::: ::::::::::::::::::::::: :::::: d1j31a_ 104 PRGYIGKYRKIHLF----YREKVFFEPGDlGFKVFDIGFAKVGVMICFDWFFP-ESARTL 158 query 176 RSAGAGLLLSVNASPYErdkddTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVV 235 ::::::::::::::::: :::::::::::::::::::::::::::::::::::::: d1j31a_ 159 ALKGAEIIAHPANLVMP-----YAPRAMPIRALENRVYTITADRVGEERGLKFIGKSLIA 213 query 236 DRDGEVVARAPQFSEGCVVLDLDLPaaeaepptgvvddglridrlviseeplpayeaela 295 ::::::::::::::::::::::::: d1j31a_ 214 SPKAEVLSIASETEEEIGVVEIDLN----------------------------------- 238 query 296 ggyadrldadeevysalvvglrayvakngfrsvliglsggidsalvaaiacdalgaqnvy 355 d1j31a_ 239 ------------------------------------------------------------ 239 query 356 gvsmpskyssdhskgdaaelarrtglnfrtvsiepmfdaymaslgltglaeenlqsrlrg 415 d1j31a_ 239 ------------------------------------------------------------ 239 query 416 ttlmaisnqeghivlapgnkselavgystlygdsvgaygpikdvyktsifrlaewrnraa 475 d1j31a_ 239 ------------------------------------------------------------ 239 query 476 aergqtppipeasitkpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtae 535 d1j31a_ 239 ------------------------------------------------------------ 239 query 536 ykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1j31a_ 239 ---------larnkrlndmndifkdrreeyyfr 262 FAST alignment (Normalized score: 14.79 Raw score:5705.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPV--EDLALR 58 :::::::::::::::::::::::::::::::::::::::::::::::::: :::: d1j31a_ 1 --MVKVGYIQMEPKILELDKNYSKAEKLIKEASKEGAKLVVLPELFDTGYNFESREEV-- 56 query 59 SSFV---------EASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPA-GAP 108 ::::::::::::: ::::::::::::: ::: d1j31a_ 57 ----FDVAQQIPEGETTTFLMELARE------LGLYIVAGTAEKS-----------GNYL 95 query 109 RNAAAVLHR--GRVALTFAKHHLPNYGV-FDEFRYFVPGD-TMPIVRLHGVDIALAICED 164 ::::::: :::::::::::: ::::::::::: ::::::::::::::::::: d1j31a_ 96 YNSAVVV--GPRGYIGKYRKIHL-----FYREKVFFEPGDLGFKVFDIGFAKVGVMICFD 148 query 165 LWQDGGRVPAARSAGAGLLLSVNASPYERDKD-DTRLELVRKRAQEAGCTTAYLAMIGGQ 223 :::: ::::::::::::::::::::: ::::::::::::::::::::::::::: d1j31a_ 149 WFFP-ESARTLALKGAEIIAHPANLV------MPYAPRAMPIRALENRVYTITADRVGEE 201 query 224 DELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVIS 283 ::::::::::::::::::::::::::::::::::: d1j31a_ 202 RGLKFIGKSLIASPKAEVLSIASETEEEIGVVEID------------------------- 236 query 284 EEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAA 343 d1j31a_ 237 ------------------------------------------------------------ 237 query 344 IACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTG 403 d1j31a_ 237 ------------------------------------------------------------ 237 query 404 LAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTS 463 d1j31a_ 237 ------------------------------------------------------------ 237 query 464 IFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDREL 523 d1j31a_ 237 ------------------------------------------------------------ 237 query 524 VVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--------------- 568 d1j31a_ 237 ---------------------------------------------LNLARNKRLNDMNDI 251 query 569 ----------- 569 d1j31a_ 252 FKDRREEYYFR 262 TMalign alignment (TM-score: 0.39 Raw score:223.49) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1j31a_ 1 --MVKVGYIQMEPKILELDKNYSKAEKLIKEASKEGAKLVVLPELFDTGYNFESREEVFD 58 query 61 FVEAS-RTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGR 119 ::::: ::::::::::::: :: ::::::::::::: :::::::::::::: d1j31a_ 59 VAQQIPEGETTTFLMELAR-EL-GLYIVAGTAEKSG----------NYLYNSAVVVGPRG 106 query 120 VALTFAKHHLPNYGVFDEFRYFVPG-DTMPIVRLHGVDIALAICEDLWQDGGRVPAARSA 178 ::::::::::: :::::::::: ::::::::::::::::::::::::: :::::::: d1j31a_ 107 YIGKYRKIHLF----YREKVFFEPGDLGFKVFDIGFAKVGVMICFDWFFPE-SARTLALK 161 query 179 GAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRD 238 :::::::::::::: ::::::::::::::::::::::::::::::::::::::::: d1j31a_ 162 GAEIIAHPANLVMP-----YAPRAMPIRALENRVYTITADRVGEERGLKFIGKSLIASPK 216 query 239 GEVVARAPQFSEGCVVLDLDLP-AAE--------------AEPPTGVVD-----DGLRID 278 :::::::::::::::::::::: ::: : d1j31a_ 217 AEVLSIASETEEEIGVVEIDLNLARNKRLNDMNDIFKDRR--------EEYYFR------ 262 query 279 RLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDS 338 d1j31a_ 263 ------------------------------------------------------------ 263 query 339 ALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMAS 398 d1j31a_ 263 ------------------------------------------------------------ 263 query 399 LGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKD 458 d1j31a_ 263 ------------------------------------------------------------ 263 query 459 VYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAG 518 d1j31a_ 263 ------------------------------------------------------------ 263 query 519 YDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1j31a_ 263 -------------------------------------------------- 263 HHsearch alignment (Probability: 1.00 E-value:0.00) query 4 LRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSSFVE 63 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1j31a_ 2 VKVGYIQMEPKILELDKNYSKAEKLIKEASKEGAKLVVLPELFDTGYNFESREEVFDVAQ 61 query 64 A-----SRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRG 118 : ::::::::::: :::::::::::::: ::::::::::::: d1j31a_ 62 QIPEGETTTFLMELARE------LGLYIVAGTAEKSG----------NYLYNSAVVVGPR 105 query 119 RVALTFAKHHLPNYGVFDEFRYFVPGDT-MPIVRLHGVDIALAICEDLWQDGGRVPAARS 177 :::::::::::: :::::::::::: ::::::::::::::::::::::: ::::::: d1j31a_ 106 GYIGKYRKIHLF----YREKVFFEPGDLGFKVFDIGFAKVGVMICFDWFFPE-SARTLAL 160 query 178 AGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDR 237 ::::::::::::: :::::::::::::::::::::::::::::::::::::::::: d1j31a_ 161 KGAEIIAHPANLV-----MPYAPRAMPIRALENRVYTITADRVGEERGLKFIGKSLIASP 215 query 238 DGEVVARAPQFSEGCVVLDLDLPAAEAEPP--TGVVDDGLRID 278 :::::::::::::::::::::::::::::: ::::::::::: d1j31a_ 216 KAEVLSIASETEEEIGVVEIDLNLARNKRLNDMNDIFKDRREE 258
Intermediate <-- 1.000 --> HitDALI alignment (Z-score: 33.2 Raw score:3144.00) d1j31a_ 1 --------MVKVGYIQMEPKILELDKNYSKAEKLIKEASKEG--AKLVVLPELFDTGYNF 50 :::::::::::::::::::::::::::::::::: :::::::::::::::: d1f89a_ 1 saskilsqKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQpdTKLVVLPECFNSPYST 60 d1j31a_ 51 EsreEVFDVA-QQIP--EGETTTFLMELARELGLYIV-AGTAEKSG--NYLYNSAVVVGP 104 : :::::: :::: :::::::::::::::::::: :::::::: :::::::::::: d1f89a_ 61 D---QFRKYSeVINPkePSTSVQFLSNLANKFKIILVgGTIPELDPktDKIYNTSIIFNE 117 d1j31a_ 105 R-GYIGKYRKIHLfYREKVFFEPGDlGFKVFDIGFAKVGVMICFDWFFPESARTLALKGA 163 : ::::::::::: ::::::::::: :::::::::::::::::::::::::::::::::: d1f89a_ 118 DgKLIDKHRKVHL-FHESETLSPGE-KSTTIDTKYGKFGVGICYDMRFPELAMLSARKGA 175 d1j31a_ 164 EIIAHPANLV----MPYAPRAMPIRALENRVYTITADRVGEE-RGLKFIGKSLIASPKAE 218 :::::::::: :::::::::::::::::::::::::::: ::::::::::::::::: d1f89a_ 176 FAMIYPSAFNtvtgPLHWHLLARSRAVDNQVYVMLCSPARNLqSSYHAYGHSIVVDPRGK 235 d1j31a_ 219 VLSIASEtEEEIGVVEIDLNLAR-NKRLndmnDIFKdRREEYyfr 262 ::::::: ::::::::::::::: :::: :::: ::::: d1f89a_ 236 IVAEAGE-GEEIIYAELDPEVIEsFRQA----VPLT-KQRRF--- 271 FAST alignment (Normalized score: 23.43 Raw score:6244.00) d1j31a_ 1 --------MVKVGYIQMEPK--ILELDKNYSKAEKLIKEASK--EGAKLVVLPELFDTGY 48 :::::::::: :::::::::::::::::::: :::::::::::::::: d1f89a_ 1 SASKILSQKIKVALVQLS--GSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPY 58 d1j31a_ 49 NFESREEVFDVAQQIP-------EGETTTFLMELARELGLYIV-AGTAEKS--GNYLYNS 98 : :::::::: :::::::::::::::::::: ::::::: ::::::: d1f89a_ 59 S---TDQFRKYS----EVINPKEPSTSVQFLSNLANKFKIILVGGTIPELDPKTDKIYNT 111 d1j31a_ 99 AVVVGPR-GYIGKYRKIHLFYREKVFFEPGDLGFKVFDIGFAKVGVMICFDWFFPESART 157 ::::::: ::::::::: ::::::::::::: :::::::::::::::::::::::::::: d1f89a_ 112 SIIFNEDGKLIDKHRKV-HLFHESETLSPGE-KSTTIDTKYGKFGVGICYDMRFPELAML 169 d1j31a_ 158 LALKGAEIIAHPANLV-----MPYAPRAMPIRALENRVYTITADRVGEE-----RGLKFI 207 ::::::::::::::: :::::::::::::::::::::::: :::::: d1f89a_ 170 SARKGAFAMIYPSAF-NTVTGPLHWHLLARSRAVDNQVYVMLCSP----ARNLQSSYHAY 224 d1j31a_ 208 GKSLIASPKAEVLSIASETEEEIGVVEIDLNLARNKRLNDMNDIF-------KDRREEYY 260 ::::::::::::::::: :::::::::::::::: ::::: d1f89a_ 225 GHSIVVDPRGKIVAEAG-EGEEIIYAELDPEVIE-----------SFRQAVPLTKQR--- 269 d1j31a_ 261 FR-- 262 d1f89a_ 270 --RF 271 TMalign alignment (TM-score: 0.89 Raw score:232.42) d1j31a_ 1 --------MVKVGYIQMEPKILELDKNYSKAEKLIKEASK-E-GAKLVVLPELFDTGYNF 50 :::::::::::::::::::::::::::::::: : ::::::::::::::::: d1f89a_ 1 SASKILSQKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPYST 60 d1j31a_ 51 ESREEVFDVA-QQIP--EGETTTFLMELARELGLYIV-AGTAEKSG--NYLYNSAVVVGP 104 : :::::: :::: :::::::::::::::::::: :::::::: :::::::::::: d1f89a_ 61 -D--QFRKYSEVINPKEPSTSVQFLSNLANKFKIILVGGTIPELDPKTDKIYNTSIIFNE 117 d1j31a_ 105 R-GYIGKYRKIHLFYREKVFFEPGDLGFKVFDIGFAKVGVMICFDWFFPESARTLALKGA 163 : ::::::::::: ::::::::::: :::::::::::::::::::::::::::::::::: d1f89a_ 118 DGKLIDKHRKVHL-FHESETLSPGE-KSTTIDTKYGKFGVGICYDMRFPELAMLSARKGA 175 d1j31a_ 164 EIIAHPANLV--MP--YAPRAMPIRALENRVYTITADRV-GEERGLKFIGKSLIASPKAE 218 :::::::::: :: ::::::::::::::::::::::: :::::::::::::::::::: d1f89a_ 176 FAMIYPSAFNTVTGPLHWHLLARSRAVDNQVYVMLCSPARNLQSSYHAYGHSIVVDPRGK 235 d1j31a_ 219 VLSIASETEEEIGVVEIDLNLARNKRLNDMNDIFKDRREEYYFR 262 ::::::: :::::::::::::::::::: ::: :::: :: d1f89a_ 236 IVAEAGE-GEEIIYAELDPEVIESFRQA--VPL-TKQR-RF--- 271 HHsearch alignment (Probability: 1.00 E-value:0.00) d1j31a_ 2 VKVGYIQMEPKILELDKNYSKAEKLIKEASKE--GAKLVVLPELFDTGYNFESREEVFDV 59 :::::::::::::::::::::::::::::::: :::::::::::::::::::::::::: d1f89a_ 10 IKVALVQLSGSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPYSTDQFRKYSEV 69 d1j31a_ 60 AQQIPEGETTTFLMELARELGLYIVAGTA---EKSGNYLYNSAVVVGPRG-YIGKYRKIH 115 ::::::::::::::::::::::::::::: :::::::::::::::::: ::::::::: d1f89a_ 70 INPKEPSTSVQFLSNLANKFKIILVGGTIPELDPKTDKIYNTSIIFNEDGKLIDKHRKVH 129 d1j31a_ 116 LFYREKVFFEPGDLGFKVFDIGFAKVGVMICFDWFFPESARTLALKGAEIIAHPANLVMP 175 :: ::::::::::: ::::::::::::::::::::::::::::::::::::::::::::: d1f89a_ 130 LF-HESETLSPGEK-STTIDTKYGKFGVGICYDMRFPELAMLSARKGAFAMIYPSAFNTV 187 d1j31a_ 176 ----YAPRAMPIRALENRVYTITADRVGE-ERGLKFIGKSLIASPKAEVLSIASETEEEI 230 ::::::::::::::::::::::::: :::::::::::::::::::::::::: ::: d1f89a_ 188 TGPLHWHLLARSRAVDNQVYVMLCSPARNLQSSYHAYGHSIVVDPRGKIVAEAGEG-EEI 246 d1j31a_ 231 GVVEIDLNLARNKRLNDMNDIFKDRRE 257 :::::::::::::: ::::::::::: d1f89a_ 247 IYAELDPEVIESFR--QAVPLTKQRRF 271