Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate PP_4549 PP_4549 long-chain-fatty-acid/CoA ligase
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__Putida:PP_4549 Length = 565 Score = 197 bits (500), Expect = 1e-54 Identities = 156/524 (29%), Positives = 247/524 (47%), Gaps = 43/524 (8%) Query: 46 LTTHDLRLWSQRLAAGLRK-SGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTF 104 +T +L S AA L++ + L+ GDR+ + N L +PV G + AG I NP + Sbjct: 50 ITYGELYALSGAFAAWLQQHTDLKPGDRIAVQLPNVLQYPVAVFGAMRAGLIVVNTNPLY 109 Query: 105 VARELAYQLQDSGATYLLCASNSLETGLEAAKQAKLPQ------------------SHIF 146 ARE+ +Q DSGA L+C +N + + ++ + + Sbjct: 110 TAREMEHQFNDSGAKALVCLANMAHLAEKVVPKTQVRHVIVTEVADLLPPLKRLLINSVI 169 Query: 147 AYDTSIYDGVTNPQKGCAYWSDLLASEEEGAAFTWDELSTPALSSTTLALNYSSGTTGRP 206 Y + PQ ++D LA G E + A + L Y+ GTTG Sbjct: 170 KYVKKMVPAYNLPQ--AVRFNDALAL---GKGQPVTEANPQA--NDVAVLQYTGGTTGVA 222 Query: 207 KGVEISHRNYVANMLQYCHT---ASLHPDYKARLERSRWLCFLPMYHAMAQNIF-IAAAL 262 KG ++HRN VANMLQ C ++LH + + LP+YH A +A L Sbjct: 223 KGAMLTHRNLVANMLQ-CRALMGSNLHEGCEILITP------LPLYHIYAFTFHCMAMML 275 Query: 263 YRATPVYIMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGA 322 V I + D M++ +++ + F+ + + VAL + A D S++++ SG Sbjct: 276 IGNHNVLISNPRDLPAMVKELGKWKFSGFVGLNTLFVALCNNEAFRALDFSALKITLSGG 335 Query: 323 APLGREVCEEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAEISTSASVGELNANCEAKI 382 L V E + + I +G+GMTE T V NP+E + ++G + K+ Sbjct: 336 MALQLSVAERWKAVTGCA---ICEGYGMTE-TSPVAAVNPSEANQVGTIGIPVPSTLCKV 391 Query: 383 MFDGVEVKERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHV 442 + D GEL V+ P VMKGYW+ E AT E +GWL TGDIA + DG + Sbjct: 392 IDDAGNELPLGEVGELCVKGPQVMKGYWQREDATAEILDSEGWLKTGDIAVIQADGYMRI 451 Query: 443 VDRMKELIKVKGNQVAPAELEALLLEHPAISDVAVIGVV-INNDERPRAYVVLRPGQSAT 501 VDR K++I V G V P ELE +L P + A IGV + E + ++V++PG + T Sbjct: 452 VDRKKDMILVSGFNVYPNELEDVLAALPGVLQCAAIGVPDEKSGEVIKVFIVVKPGMTVT 511 Query: 502 ANEIAHYLDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQ 545 ++ ++ V+ +K + + F +++P GKILR +LR++ Sbjct: 512 KEQVMEHMRANVTGYK-VPRHIEFRDSLPTTNVGKILRRELRDE 554 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: 655 Number of extensions: 26 Number of successful extensions: 4 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: 556 Length of database: 565 Length adjustment: 36 Effective length of query: 520 Effective length of database: 529 Effective search space: 275080 Effective search space used: 275080 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: 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