Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate AO353_03315 AO353_03315 long-chain fatty acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03315 Length = 562 Score = 209 bits (532), Expect = 2e-58 Identities = 181/559 (32%), Positives = 257/559 (45%), Gaps = 59/559 (10%) Query: 21 LFERKDRAYPDDKIIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNS 80 +FER + + D T TY L S F L+ + GD +A+ PN Sbjct: 29 VFERSCKKFADRPAFSNMGVT---LTYAELERYSAAFAGYLQTQTDLLPGDRIAVQMPNV 85 Query: 81 IDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLV-------TQASVLPVAR- 132 + P+ ++G L AG + NP YT E+ Q K+S A+ LV VLP Sbjct: 86 LHYPIAVFGALRAGLIVVNTNPLYTAREMRHQFKDSGARALVYLNMFGQKVQEVLPDTEI 145 Query: 133 ----EAAKKVGMPEDRIILIGDQRDPDARVKHFTSVRNISGATRY-------RKQKITPA 181 EA MP + LI D +VK ++ A + R Q I P Sbjct: 146 QYLIEAKMGDLMPTAKGWLINTVVD---KVKKMVPTYDLPQAISFKSALRLGRGQSIKPQ 202 Query: 182 K----DVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGK-----G 232 DVA L Y+ GTTG+ KG M++H N+VAN++Q G+ G DGK G Sbjct: 203 NVSLDDVAVLQYTGGTTGLAKGAMLTHGNLVANMQQARACLGQF-----GSDGKPLLREG 257 Query: 233 DRVL-AFLPFYHIYGLTCLITQALYKGYH-LIVMSKFDIEKWCAHVQNYRCSFSYIVPPV 290 V+ A LP YHIY T + G H +++ + DI + ++N+R S + + Sbjct: 258 QEVMIAPLPLYHIYAFTANCMCMMVTGNHNVLITNPRDIAGFIKELKNWRFSALLGLNTL 317 Query: 291 VLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQ 350 + L HP D SSL++ NSG L + E I +GYGL+ETSP + Sbjct: 318 FVALMDHPNFKTLDFSSLKLTNSGGTALVKATAERWEQITGCRITEGYGLTETSPVACTN 377 Query: 351 RWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPE 410 + D + +G+VG +P K + +DG E GE GEL +KGP + GY + PE Sbjct: 378 PYGD-KSRIGTVGLPVPGTTLKVIN--DDGVEQPL---GERGELCIKGPQIMKGYWQKPE 431 Query: 411 ATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDD 470 AT L DGWF++GD+ D G I DR K++I GF V P E+E ++ + + + Sbjct: 432 ATAEVLDADGWFKSGDIAVIDPDGFVRIVDRKKDMIIVSGFNVYPNEIEDVVMAHPKVAN 491 Query: 471 VAVIGIESETHGSEVPMACVVRSAKSKSSGTS-EKDEAARIIKWLDSKVASHKRLRGGVH 529 AVIG+ E G V + V R A G S E+ +A + KV H LR Sbjct: 492 CAVIGVPDERSGEAVKLFVVAREA-----GISLEELKAYCKENFTAYKVPKHIVLR---- 542 Query: 530 FVDEIPKNPSGKILRRILK 548 + +P P GKILRR L+ Sbjct: 543 --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: 726 Number of extensions: 29 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: 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