Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate BPHYT_RS32685 BPHYT_RS32685 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__BFirm:BPHYT_RS32685 Length = 387 Score = 152 bits (383), Expect = 2e-41 Identities = 100/317 (31%), Positives = 165/317 (52%), Gaps = 16/317 (5%) Query: 45 EWYRILNKKGWAVTHWPKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTF 104 E+ L K GW P+++GG+G + + EE+ A G + Sbjct: 40 EFVDALTKAGWLAALIPQDFGGSGLGLTEASVIMEEINRAGGNSGACHGQMYNMGTLLRH 99 Query: 105 GSEEQKKRFLPRIANVD-DWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLA 163 GSEEQK+++LP+IA D G +EP +G+D +KT AE++GD+++INGQK W + Sbjct: 100 GSEEQKQKYLPKIACGDLRLQSMGVTEPSTGTDTTKIKTTAERRGDRYVINGQKVWISRV 159 Query: 164 QHADWIFCLCRTDPAA---KKQEGISFILVDMKT---KGITVRPIQTIDGGHEVNEVFFD 217 QH+D + L RT P A KK EG+S +VD++ G+TV+PI + HE NE+FFD Sbjct: 160 QHSDLMILLARTTPLADVKKKSEGMSIFIVDLREAIGHGMTVQPILNM-VNHETNELFFD 218 Query: 218 DVEVPLENLVGQENKGWDYAKFLLGNERTGIAR--VGMSKERIRRIKQLAAQVESGGKPV 275 ++E+P ENL+G+E +G+ Y L ERT IA +G + ++ + A + G+P+ Sbjct: 219 NLEIPAENLIGEEGQGFKYILDGLNAERTLIAAECIGDGYWFVDKVTEYAKERVVFGRPI 278 Query: 276 IEDPKFRDKLAAVEIELKALELTQLRVVADEGKHGKGKPNPA-SSVLKIKGSEIQQATTE 334 ++ + +A + ++A L + H +P A +++ K+ ++ Sbjct: 279 GQNQGVQFPIARSFVNVEAASLMRFEAARRFDAH---QPCGAQANMAKLLAADASWEAAN 335 Query: 335 LLMEVIG--PFAAPYDV 349 ++ G FA YDV Sbjct: 336 ACLQFHGGFGFACEYDV 352 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: 19 Number of successful extensions: 4 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: 396 Length of database: 387 Length adjustment: 31 Effective length of query: 365 Effective length of database: 356 Effective search space: 129940 Effective search space used: 129940 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 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