Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate Echvi_2567 Echvi_2567 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__Cola:Echvi_2567 Length = 559 Score = 156 bits (394), Expect = 2e-42 Identities = 146/518 (28%), Positives = 239/518 (46%), Gaps = 34/518 (6%) Query: 46 LTTHDLRLWSQRLAAGLRKS-GLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTF 104 ++ H++ S+ A+ L+ L++GDR+ + N L +PV G + AG I NP + Sbjct: 50 ISFHEVDRLSKDFASYLQNELKLKKGDRIAIQMPNLLQYPVAMFGALRAGLIVVNTNPLY 109 Query: 105 VARELAYQLQDSGATYLLCASNSLETGLEAAKQAKLPQSHIFAYDTSIYDGVTNPQKGCA 164 E+ +Q +D+ + ++ +N + LE +L HI T I D + + G Sbjct: 110 TPHEMEHQFKDADISAVVIVAN-FASNLEEILP-RLDVKHIIL--TEIGDMLGGLKGGIV 165 Query: 165 -----YWSDLLASEEEGAAFTWDEL----STPALSSTTLALN------YSSGTTGRPKGV 209 Y ++ + A +++ S L TL LN Y+ GTTG KG Sbjct: 166 NLVVKYIKKMVPAYNLPNAVKFNDALDIGSHLDLQPVTLDLNDTAYLQYTGGTTGVSKGA 225 Query: 210 EISHRNYVANMLQYCHTASLHPDYKARLERSRWLCFLPMYHAMAQNIFIAAAL-YRATPV 268 ++H N +ANM Q +A + P K E + LPMYH A + A L A + Sbjct: 226 ALTHGNIIANMQQI--SAWMRPKLKEGEELV--ITALPMYHIFALTVNCLAMLKIGAHNL 281 Query: 269 YIMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGRE 328 I + D + ++ + + V + L + D S +++ G + + Sbjct: 282 LITNPRDMKAFCKDLRKHKFSVITGVNTLFNGLLNQESFRNLDFSYLKISVGGGMAVQKY 341 Query: 329 VCEEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAE-ISTSASVGELNANCEAKIMFDGV 387 V E+ + + +G+G+TE T V NP + ++G N E KI+ D Sbjct: 342 VAEKWNAVTGTP---LAEGYGLTE-TSPVACCNPIDGTERIGTIGLPLPNTEVKIIDDEG 397 Query: 388 EVKERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMK 447 +GEL ++ P VMKGYW K T + + WL TGDI + +DG +VDR K Sbjct: 398 NELPNGEKGELCIKGPQVMKGYWNKPKETNDVMLGE-WLKTGDIGIITNDGFIKIVDRKK 456 Query: 448 ELIKVKGNQVAPAELEALLLEHPAISDVAVIGVV-INNDERPRAYVVLRPGQSATANEIA 506 E+I V G V P E+E + H + +V VIG+ ++ E+ AYVV S TA+EI Sbjct: 457 EMILVSGFNVYPNEVEDAIATHDKVMEVGVIGMPDEHSTEKVIAYVVAN-DPSVTASEII 515 Query: 507 HYLDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLRE 544 + ++ +K + V F++ +PK+ GKILR ++E Sbjct: 516 KHCRESLTNYK-VPREVYFVDELPKSNVGKILRRIIKE 552 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: 658 Number of extensions: 41 Number of successful extensions: 5 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: 559 Length adjustment: 36 Effective length of query: 520 Effective length of database: 523 Effective search space: 271960 Effective search space used: 271960 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