Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate Ga0059261_0835 Ga0059261_0835 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__Korea:Ga0059261_0835 Length = 582 Score = 215 bits (547), Expect = 4e-60 Identities = 160/513 (31%), Positives = 246/513 (47%), Gaps = 41/513 (7%) Query: 57 RLAAGLRKSGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTFVARELAYQLQDS 116 RLA LR+ G+ +GDRV L N +PVVF + G I N + + EL Y L+DS Sbjct: 88 RLATQLREMGVGKGDRVALAMRNLPEWPVVFFAAVSIGAILVPLNAWWTSGELDYGLRDS 147 Query: 117 GATYLLCASNSLETGLEAAKQAKLPQ-SHIFAYDTSIYDGVTNPQ-KGCAYWSDLLASEE 174 G+ L + +A LP HI + P +G DL+ Sbjct: 148 GSVVLFTDGERYDRLADALPG--LPDLKHI------VVSRARGPLGEGVRQLEDLI---- 195 Query: 175 EGAAFTWDELSTPALSSTT-------LALNYSSGTTGRPKGVEISHRNYVANMLQ----- 222 G W EL L + + Y+SGTTG PKG +HRN + N+L Sbjct: 196 -GKPGDWAELPDAPLPAEPSLVPDDDATIFYTSGTTGHPKGALGTHRNLITNILSSGYCG 254 Query: 223 ---YCHTASLHPDYKARLERSRWLCFLPMYHAMAQNIFIAAALYRATPVYIMSKFDFVKM 279 Y + PD R+ L +P++H A + + A++ M K+D + Sbjct: 255 ARPYLRRGEMPPDPTPRVG----LMVIPLFHVTACSASLMGAVFAGHTTIFMRKWDVEQA 310 Query: 280 LEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGREVCEEVEKLWPP 339 +E QR ++ VP + L +HPA +YDLSS+E++ G AP E+ V++++ Sbjct: 311 MEIIQREKVNLTGGVPTIAWQLLEHPARAKYDLSSLEMIAYGGAPSAPEL---VKRIYTE 367 Query: 340 GKINIKQGWGMTEATCSVTGWNPAE-ISTSASVGELNANCEAKIM-FDGVEVKERNSRGE 397 GWGMTE +VT + + ++ S G E KIM +G GE Sbjct: 368 FGALPGNGWGMTETMATVTQHSAEDYLNRPTSAGPPVPVAELKIMDAEGEHELPIGEVGE 427 Query: 398 LWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMKELIKVKGNQV 457 LW + P ++KGYW + T E+ DGW+ TGD+A VD++G +VDR K++I G + Sbjct: 428 LWAKGPMIVKGYWNKPEETAES-FRDGWVRTGDLARVDEEGFLFIVDRAKDIIIRGGENI 486 Query: 458 APAELEALLLEHPAISDVAVIGVVINN-DERPRAYVVLRPGQSATANEIAHYLDNKVSAF 516 +E+E +L HPA++D A+IG+ E P A V L PG+ A+ E+ ++ ++++AF Sbjct: 487 YSSEVEDVLYAHPAVTDAALIGIPHRTLGEEPVAVVHLAPGKQASEAELQQWVRDRLAAF 546 Query: 517 KRITGGVVFLEAIPKNPSGKILRMKLREQAKEE 549 K + +P+N +GKIL+ L+ EE Sbjct: 547 KVPVAIRFTRDTLPRNANGKILKKDLKGLFAEE 579 Lambda K H 0.319 0.134 0.403 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 713 Number of extensions: 34 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 556 Length of database: 582 Length adjustment: 36 Effective length of query: 520 Effective length of database: 546 Effective search space: 283920 Effective search space used: 283920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory