Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_010960838.1 MCA_RS07725 long-chain fatty acid--CoA ligase
Query= BRENDA::D3GE78 (556 letters) >NCBI__GCF_000008325.1:WP_010960838.1 Length = 510 Score = 196 bits (499), Expect = 1e-54 Identities = 162/503 (32%), Positives = 238/503 (47%), Gaps = 33/503 (6%) Query: 55 SQRLAAGLRKSGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTFVARELAYQLQ 114 S +AAGL G+ +G+R+ L+ N + F + + G++ AG + N A E+ Y L Sbjct: 38 SDAIAAGLAVRGVAKGERIGLYCINSVEFTLAYAGIVKAGAVVVPINLLLSAEEVHYNLA 97 Query: 115 DSGATYLLCASNSLETGLEAAKQAKLPQSHIFAYDTSIYDGVTNPQKGCAYWSDLLASEE 174 D+G + L+ A + + G+ + W LL Sbjct: 98 DAGVSGLIYHGQVSANAAAVADRLS---------GLKVRAGIGLDDQDGDVWRALLEESA 148 Query: 175 EGAAFTWDELSTPALSSTTLALNYSSGTTGRPKGVEISHRNYVANMLQYCHTASLHPDYK 234 E + +D + A A+ Y+SGTTG PKG ++H N +AN T S+ Sbjct: 149 EPPSIEFDAVEDLA------AILYTSGTTGHPKGAMLTHGNLLAN------TTSVREALD 196 Query: 235 ARLERSRWLCFLPMYHAMAQNIFIAAALYRATPVYIMSKFDFVKMLEYTQRFRITDFILV 294 R R L LPM+HA A + + L + ++KF+ ++ + R R T F+ V Sbjct: 197 WRPGEDRVLVVLPMFHAFAATVGMLTPLLHGCALIPLAKFEPDRVADTIGRHRATLFLGV 256 Query: 295 PPVVVALAKHPAVGQYDLSSVELVGSGAAPLGREVCEEVEKLWPPGKINIKQGWGMTEAT 354 P + L + +V L SG A L V E+ + + + I +G G TE + Sbjct: 257 PSMYALLCRLGEERIARFGTVRLCVSGGAALPPSVMEQFQARFG---LPIHEGDGPTECS 313 Query: 355 CSVTGWNP-AEISTSASVGELNANCEAKIMF-DGVEVKERNSRGELWVRAPNVMKGYWRN 412 VT NP A +VG E KI+ DGVE+ R GE+ VR NV KGYW Sbjct: 314 -PVTCVNPVAGPVKRGTVGLPVPGVEMKILGEDGVELP-RGELGEIAVRGANVFKGYWNQ 371 Query: 413 EKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMKELIKVKGNQVAPAELEALLLEHPAI 472 +AT+E DGW LTGD+ VDDDG F +VDR K+LI V G V P +E +L HPA+ Sbjct: 372 PEATREC-FRDGWFLTGDLGQVDDDGYFSIVDRKKDLIIVNGMNVYPRVIEEVLCRHPAV 430 Query: 473 SDVAVIGVVIN-NDERPRAYVVLRPGQSATANEIAHYLDNKVSAFKRITGGVVFLEAIPK 531 +VAV+G + ER AYVVL A+ EI + + + I V L+ +P+ Sbjct: 431 REVAVVGDPDPLHGERVVAYVVL--DAPASEAEIRAWCKPYLGRHE-IPRQVKALQQLPR 487 Query: 532 NPSGKILRMKLREQAKEELRVTA 554 N +GKI++ +LR Q + E V A Sbjct: 488 NAAGKIVKRQLRRQGEVERGVDA 510 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: 574 Number of extensions: 33 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 556 Length of database: 510 Length adjustment: 35 Effective length of query: 521 Effective length of database: 475 Effective search space: 247475 Effective search space used: 247475 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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