Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate WP_043745120.1 AMB_RS18150 acyl-CoA dehydrogenase
Query= reanno::ANA3:7025618 (385 letters) >NCBI__GCF_000009985.1:WP_043745120.1 Length = 378 Score = 459 bits (1182), Expect = e-134 Identities = 225/376 (59%), Positives = 277/376 (73%) Query: 1 MDFNFNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG 60 MDF DQ F A FA E+AP AA WDEE FP+D ++KA ELGF +Y E G Sbjct: 1 MDFGLTPDQEAFRQAAHDFAVGEMAPHAAHWDEEGIFPEDTLRKAAELGFAGIYVGEDVG 60 Query: 61 GMGLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQMLA 120 G LSRLDA++IFEEL+ C +T A ++IHNMA WM+ ++G R+ + L + + A Sbjct: 61 GSALSRLDAALIFEELAAACPSTAAYISIHNMAAWMIDSFGDQEQRRRFLPDLCSMRKFA 120 Query: 121 SYCLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTGQAGPKGIS 180 SYCLTEP AGSDAASL+TKA R+GD YV++G+K FISG G +++ VVM RTG GPKGIS Sbjct: 121 SYCLTEPNAGSDAASLRTKAERDGDHYVLNGTKAFISGGGRSDVYVVMVRTGAPGPKGIS 180 Query: 181 AIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDGG 240 + + A + G+ +GK E K+GW QPT V F++ RVPVAN +G EG GF AMKGLDGG Sbjct: 181 CLVVEAGTPGLSFGKQEKKLGWKTQPTASVIFEDCRVPVANRIGAEGDGFKIAMKGLDGG 240 Query: 241 RINIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRLA 300 RINI CS+G A+A LE A +Y +RQQFG+ ++AFQA QFKLADMATEL AAR M+ A Sbjct: 241 RINIGACSLGGARACLEHAIEYTGQRQQFGQAISAFQATQFKLADMATELEAARLMIHRA 300 Query: 301 AFKLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQI 360 A LDS P+AT +CAMAKR ATDVGF V DAALQ+HGGYGYI+EYP+ER+FRD+RVHQI Sbjct: 301 AHSLDSKSPQATVHCAMAKRMATDVGFAVTDAALQLHGGYGYIKEYPIERYFRDLRVHQI 360 Query: 361 LEGTNEIMRLIIARRL 376 LEG+NEIMR+II R L Sbjct: 361 LEGSNEIMRVIIGRAL 376 Lambda K H 0.320 0.134 0.396 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: 445 Number of extensions: 10 Number of successful extensions: 1 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: 385 Length of database: 378 Length adjustment: 30 Effective length of query: 355 Effective length of database: 348 Effective search space: 123540 Effective search space used: 123540 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 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