Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate Ac3H11_4250 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4250 Length = 546 Score = 174 bits (440), Expect = 1e-47 Identities = 146/513 (28%), Positives = 229/513 (44%), Gaps = 29/513 (5%) Query: 46 TYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYT 105 TY + S F L+ + RKGD +A+ PN + P+ M G AG NP YT Sbjct: 50 TYAHVDQQSRAFAAYLQNVLRVRKGDRIAVMCPNLVAFPIAMLGIARAGCVQVNVNPLYT 109 Query: 106 VDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRIILIGDQRDPD-------ARV 158 EL QL ++ + +V A +V + + GD D A + Sbjct: 110 PRELEHQLLDAGVRVMVVYAGSTATLAAIQDRVELHSIITVAPGDGTAADLPGPPVDAHL 169 Query: 159 KHFTSVRNI--SGATRYRKQKITPAKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFI 216 TS GAT + D+ FL Y+ GTTG+ KG M++HRN+VAN+ Q Sbjct: 170 HTTTSFARALAEGATLPFAPPVLEGGDLLFLQYTGGTTGLSKGAMLTHRNLVANVEQFKA 229 Query: 217 AEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTC-LITQALYKGYHLIVMSKFDIEKWCAH 275 + L + ++ +P YHI+ L LI+ + +V + D++ Sbjct: 230 FVPDALR------PAQEVIVTAIPLYHIFALMVNLISYFAVGARNWLVPNPRDLDALIHV 283 Query: 276 VQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIK 335 + R S V + L HP D S+LR+ G A + + + I+ Sbjct: 284 LNAARPSVFMGVNTLYAGLAAHPGTQGVDFSNLRLAGGGGAAILSSVSARWQAITGQFIR 343 Query: 336 QGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELY 395 +GYGLSETSP GS G +P+ + +D P V G+ GE+ Sbjct: 344 EGYGLSETSPVVAFNP-ASVTAFSGSTGLPLPSTDVLLL---DDQGHP--VPLGQPGEVC 397 Query: 396 LKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPP 455 +KGP V GY + PEA + DG+F+TGD+G D +G I DR K+++ GF V P Sbjct: 398 VKGPQVMGGYWQQPEANAVAFTPDGYFRTGDIGQLDERGFLKIVDRKKDMVIVSGFNVFP 457 Query: 456 AELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLD 515 E+E + + A IG+ + G + + V +++GT+ +A +I Sbjct: 458 NEIEAVATACPGVLECACIGVSDDKTGEALRLYVV------RAAGTAPPVDADQIAAHCR 511 Query: 516 SKVASHKRLRGGVHFVDEIPKNPSGKILRRILK 548 + + ++K R + F++ +PK+ GKILRR L+ Sbjct: 512 AALTAYKVPR-QIVFLEALPKSSVGKILRRELR 543 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: 667 Number of extensions: 34 Number of successful extensions: 6 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: 546 Length adjustment: 36 Effective length of query: 526 Effective length of database: 510 Effective search space: 268260 Effective search space used: 268260 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: 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