Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_034268902.1 AMYHA_RS06270 acyl-CoA dehydrogenase family protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >NCBI__GCF_000504245.1:WP_034268902.1 Length = 381 Score = 307 bits (787), Expect = 3e-88 Identities = 169/375 (45%), Positives = 232/375 (61%), Gaps = 2/375 (0%) Query: 1 MIPNDDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGC 60 ++P+ + + + + R+ A++ L P A E+++ RFP+E + G G+ E+WGG Sbjct: 6 LLPSTEAEDLLALTREIARDELAPRADEYEQAERFPREQFRLLGKSGLLGLPYAERWGGG 65 Query: 61 DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGA 120 D Y Y LEEIA+ + +SVH ++ C + YGTDEQ++R+L L G +LGA Sbjct: 66 DVPYEVYLQVLEEIASAWMSVGVGLSVH-TMSCFALAFYGTDEQRDRWLPDLLGGDLLGA 124 Query: 121 FALTEPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGIS 180 +AL+E AGSDA+ L TRA +GD YV+NG K +IT G A T P AG +GIS Sbjct: 125 YALSETHAGSDAAALSTRAVRDGDEYVVNGTKAWITHGGKADFYTTMVRTSP-AGSKGIS 183 Query: 181 AFIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGG 240 +V D+PG A E K+G AS T Q++F D +VP LGEEG G RIAL +L G Sbjct: 184 CLLVAADTPGLSAATPERKMGMTASTTSQMIFSDARVPTDRLLGEEGAGLRIALDSLASG 243 Query: 241 RVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300 R+GIA+ +VG+A+AA + A YA ER FGK II+ Q V F LADMA + +R A Sbjct: 244 RLGIAACAVGLAQAALDEAVRYATERTQFGKSIIDFQGVEFLLADMAAAVESSRATYLEA 303 Query: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIY 360 A +D G P +AS+AKL A++ A KV + A+Q LGG GY DFPVER R+ +V QI+ Sbjct: 304 ARRKDRGLPFARQASIAKLVATDSAMKVTTDAVQVLGGAGYTKDFPVERYMREAKVPQIF 363 Query: 361 EGTSDIQRMVISRNL 375 EGT+ IQRMVI++ L Sbjct: 364 EGTNQIQRMVIAKEL 378 Lambda K H 0.320 0.135 0.394 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: 326 Number of extensions: 16 Number of successful extensions: 3 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: 375 Length of database: 381 Length adjustment: 30 Effective length of query: 345 Effective length of database: 351 Effective search space: 121095 Effective search space used: 121095 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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