Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate WP_058929097.1 AU252_RS00805 acyl-CoA dehydrogenase family protein
Query= metacyc::MONOMER-20676 (396 letters) >NCBI__GCF_001484605.1:WP_058929097.1 Length = 381 Score = 95.1 bits (235), Expect = 3e-24 Identities = 89/343 (25%), Positives = 153/343 (44%), Gaps = 30/343 (8%) Query: 60 WPKEYGGTGWSSVQHYIFNEELQAAPAPQPLA--FGVSMVGPVIYTFGSEEQKKRFLPRI 117 +P GG G +F + + + LA F ++ P + GSE+ +R++ Sbjct: 58 FPDALGGGGTQLDLMTVFEQMIHSGVPTGVLASLFSHTIALPSLVKHGSEDLHRRYVIPT 117 Query: 118 ANVDDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDP 177 + G +EPG GSD+A+L+TKA + GD ++ING KT+ T AD++ RT Sbjct: 118 LEGEMIGALGLTEPGGGSDVAALRTKAVRDGDHYVINGSKTFITSGVRADFVTVAARTGA 177 Query: 178 AAKKQEGISFILVDMKTKGITV-RPIQTIDG-GHEVNEVFFDDVEVPLENLVGQENKGWD 235 + K GIS +VD T G TV R ++ + + E+ F DV VP NL+GQEN G+ Sbjct: 178 SGNK--GISLFVVDADTPGFTVSRKLEKMGWLSSDTAELSFVDVRVPASNLIGQENGGFR 235 Query: 236 YAKFLLGNERTGIA--RVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELK 293 L +ER +A +++ + + + G+P+ R K+A + + Sbjct: 236 QLMEQLQSERLTMAVECTAVARRCLDLTIEWVRNRHTFGEPLSSRQVVRHKIAEM---AR 292 Query: 294 ALELTQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLM-EVIGPFAAPYDVHGD 352 ++ V + + G + +TE+ M + +A Y H Sbjct: 293 QTDVASNYVWSTATRWAAG----------------EDVSTEVAMAKNTAVYAVEYVAHEA 336 Query: 353 DDSNETMDW--TAQIAPGYFNNRKVSIYGGSNEIQRNIICKAV 393 + M + ++ Y + R + I GG+NEI ++I K + Sbjct: 337 VQLHGGMGFMRECEVERHYRDIRVMGIGGGTNEIMNDVIAKRI 379 Lambda K H 0.317 0.135 0.411 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: 347 Number of extensions: 15 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: 396 Length of database: 381 Length adjustment: 30 Effective length of query: 366 Effective length of database: 351 Effective search space: 128466 Effective search space used: 128466 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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