Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_007473537.1 CMTB2_RS01995 long-chain fatty acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_000170735.1:WP_007473537.1 Length = 519 Score = 200 bits (508), Expect = 1e-55 Identities = 152/488 (31%), Positives = 243/488 (49%), Gaps = 39/488 (7%) Query: 68 RKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASV 127 +KGD + ++ NS++ + ++G G P N DE++F L + A+ L+ + Sbjct: 54 KKGDKIPIYVNNSLEFVIALFGIQKIGAVPVPINTFLKEDEISFILNDIEAEFLIASSKF 113 Query: 128 LPVAREAAKKVGMPEDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAKDVAFL 187 +K + +II G+ D FT + +S + + D+A + Sbjct: 114 EKNIPNIREKTSVK--KIIWEGEPSIIDEDNISFTEI--LSNIEPHESIEYPTLDDLAVI 169 Query: 188 VYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGK---GDRVLAFLPFYHI 244 +Y+SGTTG PKG M++++NI A+I W K DR +A+LP +H Sbjct: 170 IYTSGTTGKPKGAMLTYKNIFADI------------WGINEIVKITPKDRFIAYLPMFHS 217 Query: 245 YGLTCLITQALYKGYHLIVM-SKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKY 303 + +T I LY G ++++ S R + VP V L + + + Sbjct: 218 FTMTVNILLPLYTGSAVVIIKSIMPFSNIIKQTLLKRVTIFTGVPDVYSALSRAKLPFYF 277 Query: 304 D-LSSLRMMNSGAAPLTQELVEAVYSRIKVG-IKQGYGLSETSPTTHSQRWEDWREAMGS 361 + +R SGAA L E++E + K + +GYGLSETSP R + + GS Sbjct: 278 HWFNKVRFYVSGAAALPGEVLERFSKKFKKAKLLEGYGLSETSPVVAVNR--PYLQKPGS 335 Query: 362 VGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGW 421 VG +P ++ K + E EV GE GE+ +KG V GY+ EA + CL +GW Sbjct: 336 VGPAIPGVEVKIVN-----DELIEVPIGEAGEIIVKGDIVMKGYYNRDEANEECLI-NGW 389 Query: 422 FQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETH 481 F TGD+G D G YI DR K+LI KG + P E+E ++ I D AV+G++ E H Sbjct: 390 FLTGDIGKVDEDGFIYILDRKKDLIISKGVNIYPREIEEIILKFPGIKDCAVVGLKDENH 449 Query: 482 GSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGK 541 G E+P+A + + +EKD + K+L SK+A++K L ++FV+ +PKN +GK Sbjct: 450 G-EIPVAFI---EVEEDMEVNEKD----LRKYLKSKLANYK-LPKYIYFVENLPKNATGK 500 Query: 542 ILRRILKQ 549 +L+RIL++ Sbjct: 501 VLKRILRE 508 Lambda K H 0.317 0.136 0.410 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: 683 Number of extensions: 40 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 562 Length of database: 519 Length adjustment: 35 Effective length of query: 527 Effective length of database: 484 Effective search space: 255068 Effective search space used: 255068 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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