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 | d1f89a_ | hypothetical protein yl85 | Carbon-nitrogen hydrolase | Carbon-nitrogen hydrolase | α+β |
| Hit | d1cr1a_ | Gene 4 protein (g4p, DNA primase), helicase domain | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | α/β |
Query <-- 1.412 --> IntermediateDALI alignment (Z-score: 26.4 Raw score:2649.90) query 1 ------SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQG--AHLVAFPEMALTGYpV 52 :::::::::::::::::::::::::::::::::::: :::::::::::::: : d1f89a_ 1 saskilSQKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQpdTKLVVLPECFNSPY-S 59 query 53 EDLALRssFVEASR----TALRELAARLAeeGFGELPVLV-GYLDRSESaqpkygqpAGA 107 :::::: :::::: ::::::::::: ::::::::: :::::::: ::: d1f89a_ 60 TDQFRK--YSEVINpkepSTSVQFLSNLA--NKFKIILVGgTIPELDPK--------TDK 107 query 108 PRNAAAVLH-RGRVALTFAKHHLpnygvfDEFRYFVPGDTMPIVRLHGVDIALAICEDLW 166 ::::::::: ::::::::::::: ::::::::::::::::::::::::::::::: d1f89a_ 108 IYNTSIIFNeDGKLIDKHRKVHL-----fHESETLSPGEKSTTIDTKYGKFGVGICYDMR 162 query 167 QDgGRVPAARSAGAGLLLSVNASPYErdkDDTRLELVRKRAQEAGCTTAYLAMIGGQ-DE 225 :: ::::::::::::::::::::::: :::::::::::::::::::::::::::: :: d1f89a_ 163 FP-ELAMLSARKGAFAMIYPSAFNTV-tgPLHWHLLARSRAVDNQVYVMLCSPARNLqSS 220 query 226 LVFDGDSIVVDRDGEVVARAPqFSEGCVVLDLDLPaaeaepptgvvddglridrlvisee 285 ::::::::::::::::::::: ::::::::::::: d1f89a_ 221 YHAYGHSIVVDPRGKIVAEAG-EGEEIIYAELDPE------------------------- 254 query 286 plpayeaelaggyadrldadeevysalvvglrayvakngfrsvliglsggidsalvaaia 345 d1f89a_ 255 ------------------------------------------------------------ 255 query 346 cdalgaqnvygvsmpskyssdhskgdaaelarrtglnfrtvsiepmfdaymaslgltgla 405 d1f89a_ 255 ------------------------------------------------------------ 255 query 406 eenlqsrlrgttlmaisnqeghivlapgnkselavgystlygdsvgaygpikdvyktsif 465 d1f89a_ 255 ------------------------------------------------------------ 255 query 466 rlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtgadaivaagydrelvv 525 d1f89a_ 255 ------------------------------------------------------------ 255 query 526 ktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1f89a_ 255 --------------------------viesfrqavpltkqrrf 271 FAST alignment (Normalized score: 13.47 Raw score:5287.00) query 1 ------SLQLRLALNQIDST--VGDIAGNAEAILRWTRHSAE--QGAHLVAFPEMALTGY 50 :::::::::::: :::::::::::::::::::: :::::::::::::::: d1f89a_ 1 SASKILSQKIKVALVQLS--GSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPY 58 query 51 PVEDLALRSSFV------------EASRTALRELAARLAEEGFGELPVL-VGYLDRSESA 97 ::::: ::::::::::::: :::::: :::::::: d1f89a_ 59 -STDQF------RKYSEVINPKEPSTSVQFLSNLANK------FKIILVGGTIPELDP-- 103 query 98 QPKYGQP-AGAPRNAAAV-LHRGRVALTFAKHHLPNYGVF--DEFRYFVPGDTMPIVRLH 153 :::::::::: :::::::::::::: :::::::::::::::::: d1f89a_ 104 -------KTDKIYNTSIIFNEDGKLIDKHRKVH-------LFHESETLSPGEKSTTIDTK 149 query 154 GVDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDKD-----DTRLELVRKRAQ 208 ::::::::::::::: ::::::::::::::::::::: :::::::::::: d1f89a_ 150 YGKFGVGICYDMRFP-ELAMLSARKGAFAMIYPSAFN------TVTGPLHWHLLARSRAV 202 query 209 EAGCTTAYLAMIGGQ-----DELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAE 263 ::::::::::: :::::::::::::::::::::: :::::::::::: d1f89a_ 203 DNQVYVMLCSP----ARNLQSSYHAYGHSIVVDPRGKIVAEA-GEGEEIIYAELD----- 252 query 264 AEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKN 323 d1f89a_ 253 ------------------------------------------------------------ 253 query 324 GFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNF 383 d1f89a_ 253 ------------------------------------------------------------ 253 query 384 RTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYS 443 d1f89a_ 253 ------------------------------------------------------------ 253 query 444 TLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILEL 503 d1f89a_ 253 ------------------------------------------------------------ 253 query 504 YVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNR 563 d1f89a_ 253 ------------------------------------------------------------ 253 query 564 WREGH------------------- 568 d1f89a_ 253 -----PEVIESFRQAVPLTKQRRF 271 TMalign alignment (TM-score: 0.40 Raw score:224.72) query 1 S------LQLRLALNQIDSTVGDIAGNAEAILRWTRHSAE-Q-GAHLVAFPEMALTGYPV 52 : ::::::::::::::::::::::::::::::::: : :::::::::::::::: d1f89a_ 1 SASKILSQKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPYS- 59 query 53 EDLALRSSFVEASR----TALRELAARLAEEGFGELPVLV-GYLDRSESAQPKYGQPAGA 107 :::::: :::::: :::::::::::: :: :::::: :::::::: ::: d1f89a_ 60 TDQFRK--YSEVINPKEPSTSVQFLSNLAN-KF-KIILVGGTIPELDPK--------TDK 107 query 108 PRNAAAVLH-RGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLW 166 ::::::::: ::::::::::::: :::::::::::::::::::::::::::::::: d1f89a_ 108 IYNTSIIFNEDGKLIDKHRKVHL-----FHESETLSPGEKSTTIDTKYGKFGVGICYDMR 162 query 167 QDGGRVPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGG-QDE 225 ::: :::::::::::::::::::::::: ::::::::::::::::::::::::::: ::: d1f89a_ 163 FPE-LAMLSARKGAFAMIYPSAFNTVTG-PLHWHLLARSRAVDNQVYVMLCSPARNLQSS 220 query 226 LVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDL--PA--------------AEAEPPTG 269 ::::::::::::::::::::: :::::::::::: :: d1f89a_ 221 YHAYGHSIVVDPRGKIVAEAG-EGEEIIYAELDPEVIESFRQAVPLTKQRRF-------- 271 query 270 VVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNGFRSVL 329 d1f89a_ 272 ------------------------------------------------------------ 272 query 330 IGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIE 389 d1f89a_ 272 ------------------------------------------------------------ 272 query 390 PMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDS 449 d1f89a_ 272 ------------------------------------------------------------ 272 query 450 VGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDT 509 d1f89a_ 272 ------------------------------------------------------------ 272 query 510 GADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1f89a_ 272 ----------------------------------------------------------- 272 HHsearch alignment (Probability: 1.00 E-value:0.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQ--GAHLVAFPEMALTGYPVEDLALR 58 ::::::::::::::::::::::::::::::::::: ::::::::::::::::::::::: d1f89a_ 7 SQKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPYSTDQFRKY 66 query 59 SSFVE-----ASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAA 113 ::::: :::::::::::: :::::::::::::: ::::::::::: d1f89a_ 67 SEVINPKEPSTSVQFLSNLANK------FKIILVGGTIPELD-------PKTDKIYNTSI 113 query 114 VLH-RGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRV 172 ::: ::::::::::::: ::::::::::::::::::::::::::::::::::: :: d1f89a_ 114 IFNEDGKLIDKHRKVHL-----FHESETLSPGEKSTTIDTKYGKFGVGICYDMRFPE-LA 167 query 173 PAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGG-QDELVFDGD 231 :::::::::::::::::::::: ::::::::::::::::::::::::::: ::::::::: d1f89a_ 168 MLSARKGAFAMIYPSAFNTVTG-PLHWHLLARSRAVDNQVYVMLCSPARNLQSSYHAYGH 226 query 232 SIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRI 277 :::::::::::::::: ::::::::::::::::::::::::::::: d1f89a_ 227 SIVVDPRGKIVAEAGE-GEEIIYAELDPEVIESFRQAVPLTKQRRF 271
Intermediate <-- 1.005 --> HitDALI alignment (Z-score: 3.1 Raw score:400.10) d1f89a_ 1 -------------------------------------------------------saski 5 d1cr1a_ 1 mrerirehlsseesvgllfsgctgindktlgarggevimvtsgsgmgkstfvrqqalqwg 60 d1f89a_ 6 LSQKIKVALVQL------------------------------------------------ 17 :::::::::::: d1cr1a_ 61 TAMGKKVGLAMLeesveetaedliglhnrvrlrqsdslkreiiengkfdqwfdelfgndt 120 d1f89a_ 18 -----SGSSpdkmANLQRAATFIERAMKEQPdTKLVVLPECfnspystdqfrkYSEVinp 72 :::: :::::::::::::::::: ::::::::: :::: d1cr1a_ 121 fhlydSFAE----AETDRLLAKLAYMRSGLG-CDVIILDHI-----------sIRKM--- 161 d1f89a_ 73 kepSTSVQFLSNLANKFKIILVGGTipeldpktdkiyntsiifnedgKLIDKHRKVHlfh 132 :::::::::::::::::::::: :::::::::: d1cr1a_ 162 --iDNLMTKLKGFAKSTGVVLVVIC--------hlktdlrgsgalrqLSDTIIALER--- 208 d1f89a_ 133 esetlspgEKSTTIDtkygkfgvgicydmRFPElamlsarkgafamiypsafntvtgplh 192 ::::::: :::: d1cr1a_ 209 ---nqlvlVRILKCR-----ftgdtgiagYMEY--------------------------- 233 d1f89a_ 193 whllaRSRAvdnqvyvmlcsparnlqssyhayghsivvdprgkivaeagegeeiiyaeld 252 :::: d1cr1a_ 234 ---nkETGW--------------------------------------------------- 239 d1f89a_ 253 peviesfrqavpltkqrrf 271 d1cr1a_ 240 -------------lepssy 245 FAST alignment (Normalized score: 1.90 Raw score:488.80) d1f89a_ 1 SASKILSQKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPYST 60 d1cr1a_ 1 ------------------------------------------------------------ 1 d1f89a_ 61 DQFRKYSEVINPKEP--------------------------------------------- 75 d1cr1a_ 1 ---------------MRERIREHLSSEESVGLLFSGCTGINDKTLGARGGEVIMVTSGSG 45 d1f89a_ 76 -------------------------------STSVQFLSNLANKFKIILVGGTIPELDPK 104 ::::::::::: d1cr1a_ 46 MGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLH------------------ 87 d1f89a_ 105 TDKIYNTSIIFNEDGKL---------------------------------IDKHRKVHLF 131 :::: d1cr1a_ 88 -----------------NRVRLRQSDSLKREIIENGKFDQWFDELFGNDTFHLY------ 124 d1f89a_ 132 HESETLSPGEKSTTIDTKYGKFGVGIC-----YDMR-FPELAMLSAR-KGAFAMIYPSAF 184 :::: :::::::::: ::::::::: d1cr1a_ 125 ---------------------------DSFAEAETDRLLAKLAYMRSGLGCDVIILD--- 154 d1f89a_ 185 NTVTGP--------LHWHLLARSRAVDNQVYVMLCSPARNLQSSYHAYGHSIVVDPRG-- 234 ::::::::::::::::::::::: d1cr1a_ 155 ------HISIRKMIDNLMTKLKGFAKSTGVVLVVICH---------------------LK 187 d1f89a_ 235 -----------KIVAEAGEGEEIIYAELDPEVIESFRQAVPLTKQRRF------------ 271 :::::: d1cr1a_ 188 TDLRGSGALRQLSDTII-------------------------------ALERNQLVLVRI 216 d1f89a_ 272 ----------------------------- 272 d1cr1a_ 217 LKCRFTGDTGIAGYMEYNKETGWLEPSSY 245 TMalign alignment (TM-score: 0.35 Raw score:95.32) d1f89a_ 1 --------------SASKILSQKIKVA------------------LVQLSGSSPDKMANL 28 :::::: :::::: : d1cr1a_ 1 MRERIREHLSSEES-------VGLLFSGCTGINDKTLGARGGEVIMVTSGS-------G- 45 d1f89a_ 29 QRAATFIERAMKEQ-PDTKL------V-VLPECFNSPYSTDQFRKYSEVINPKEPSTSVQ 80 ::::::: :: : :::: : :::::: ::: : ::: d1cr1a_ 46 -MGKSTFV-RQ--QA-LQWGTAMGKKVGLAMLEE--------------SVE----E-TAE 81 d1f89a_ 81 FLSNLANKF--------------------KIILVGGTIPELDPKTDKIYNTSIIFNEDGK 120 ::::::::: :::::: d1cr1a_ 82 DLIGLHNRVRLRQSDSLKREIIENGKFDQ-------------------------WFDELF 116 d1f89a_ 121 L---IDKHRKVHLFHESETLSPGEKSTTIDTKYGKFGVGICYDMRFPELAMLSARK-GAF 176 : ::::::::: :::::::::::::::: ::: d1cr1a_ 117 GNDTFHLYDSFAE---------------------------AETDRLLAKLAYMRSGLGCD 149 d1f89a_ 177 AMIYPSAFNTVTGPLHWHLLARSRAVDNQVYVMLCSPARN---LQSSYHAYGHSIVVDPR 233 ::::::::: ::::::::::::::::::::::::::: :: :::::::: d1cr1a_ 150 VIILDHISI-RKMIDNLMTKLKGFAKSTGVVLVVICH-LKTDL------RGSGALRQ--- 198 d1f89a_ 234 GKIVAEAGEGE----EIIY-AE--------------------------LDPEVIESFRQA 262 :::::::::: :::: :: d1cr1a_ 199 -LSDTIIALERNQLVLVRILKCRFTGDTGIAGYMEYNKETGWLEPSSY------------ 245 d1f89a_ 263 VPLTKQRRF 271 d1cr1a_ 246 --------- 246 HHsearch alignment (Probability: 0.38 E-value:0.00) d1f89a_ 156 GICYDMRFPELAMLSARKGAFAMIYPSAFNTVTGPLHWHLLARSRAVDNQVYVMLCSPAR 215 :::::: ::::::::::::::::::::::::: ::::::::::::::::::::::::::: d1cr1a_ 130 AETDRL-LAKLAYMRSGLGCDVIILDHISIRK-MIDNLMTKLKGFAKSTGVVLVVICHLK 187 d1f89a_ 216 NLQSSYHAYGHSIVVDPRGKIVAEAGEGE 244 ::: :::::::::::::::::::: d1cr1a_ 188 TDL------RGSGALRQLSDTIIALERNQ 210