Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate PP_4550 PP_4550 long-chain-fatty-acid/CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__Putida:PP_4550 Length = 562 Score = 190 bits (483), Expect = 1e-52 Identities = 160/535 (29%), Positives = 247/535 (46%), Gaps = 58/535 (10%) Query: 46 TYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYT 105 +Y L S F L+ + + G+ +A+ PN + P+ ++G + AG + NP YT Sbjct: 51 SYAELERHSAAFAAWLQQHTDLKPGERIAVQMPNVLQYPIAVFGAMRAGLIVVNTNPLYT 110 Query: 106 VDELAFQLKNSHAKGLV-------TQASVLP---VAREAAKKVG--MPEDRIILIGDQRD 153 E+ Q K+S A+ LV VLP + K+G +P + L+ D Sbjct: 111 EREMRHQFKDSGARALVYLNMFGKRVQEVLPDTGIEYLIEAKMGDLLPAAKGWLVNTVVD 170 Query: 154 PDARVKHFTSVRNISGATRYRK-----QKITPAK------DVAFLVYSSGTTGVPKGVMI 202 ++K + A +++ + ++P D+A L Y+ GTTG+ KG M+ Sbjct: 171 ---KLKKMVPAYRLPQAVPFKQVLREGRGLSPKPVSLNLDDIAVLQYTGGTTGLAKGAML 227 Query: 203 SHRNIVANIRQQFIAEGEMLSWNGGPDGK-----GDRVL-AFLPFYHIYGLTCLITQALY 256 +H N+VAN+ Q + GPDG+ G V+ A LP YHIY T + Sbjct: 228 THGNLVANMLQVLACFSQH-----GPDGQKLLKDGQEVMIAPLPLYHIYAFTANCMCMMV 282 Query: 257 KGYH-LIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGA 315 G H +++ + DI + + +R S + + + L HP + D S+L++ NSG Sbjct: 283 TGNHNVLITNPRDIPGFIKELGKWRFSALLGLNTLFVALMDHPGFRQLDFSALKVTNSGG 342 Query: 316 APLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMT 375 L + E I +GYGL+ETSP + + +G+VG +P + Sbjct: 343 TALVKATAERWEDLTGCRIVEGYGLTETSPVASTNPYGQLAR-LGTVG--IPVAGTAFKV 399 Query: 376 MPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGN 435 + +DG+E + GE GEL +KGP V GY + PEAT L +GWF+TGD+ D G Sbjct: 400 IDDDGNE---LPLGERGELCIKGPQVMKGYWQQPEATAQALDAEGWFKTGDIAVIDPDGF 456 Query: 436 FYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAK 495 I DR K++I GF V P E+E ++ + + + A IG+ E G V + V R Sbjct: 457 TRIVDRKKDMIIVSGFNVYPNEIEDVVMGHPKVANCAAIGVPDERSGEAVKLFVVPR--- 513 Query: 496 SKSSGTSEKDEAARIIK--WLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILK 548 G DE K + KV H LR + +P P GKILRR L+ Sbjct: 514 ---EGGLSVDELKAYCKANFTGYKVPKHIVLR------ESLPMTPVGKILRRELR 559 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: 738 Number of extensions: 27 Number of successful extensions: 6 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: 562 Length of database: 562 Length adjustment: 36 Effective length of query: 526 Effective length of database: 526 Effective search space: 276676 Effective search space used: 276676 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