Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_011912851.1 PST_RS08590 acyl-CoA dehydrogenase family protein
Query= BRENDA::Q18AQ1 (378 letters) >NCBI__GCF_000013785.1:WP_011912851.1 Length = 387 Score = 201 bits (512), Expect = 2e-56 Identities = 114/358 (31%), Positives = 203/358 (56%), Gaps = 15/358 (4%) Query: 16 VSFAENEVKPLATE--------LDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVG 67 +SF V+ L E +DEE+ FP V M +AG + P+EYGG G Sbjct: 9 LSFIREGVRALCAEFPAEYWRRIDEEKGFPEAFVTAMTEAGWLSAMIPEEYGGSGLGLAE 68 Query: 68 YIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGE-KLGAFGLTE 126 + +EE++R G +G I ++ + + + G+EEQK+ +L LA+GE +L + G+TE Sbjct: 69 ASVILEEVNRCGGNSGTIHGQMYNM--FTLLRNGSEEQKRYYLPKLANGELRLQSMGVTE 126 Query: 127 PNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMT----DKSKGNKGISA 182 P GTD + +TTAV GD+Y++NG K++I+ D+ +++A T + + ++G+S Sbjct: 127 PTTGTDTTKIKTTAVRRGDKYVINGQKVWISRIQHSDLMILLARTTPLAEVQRKSEGMSI 186 Query: 183 FIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGR 242 F+V+ + + + T+EL F++ IP +L+G+EG+GF+ + L+ R Sbjct: 187 FLVDLREAIGNGLTVQPIANMVNHETNELFFDNLEIPASSLIGEEGKGFRYILDGLNAER 246 Query: 243 IGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAA 302 IAA+ +G + ++++ +Y ++RV FGRP+ + Q QF +A+ ++++AA + ++A Sbjct: 247 TLIAAECIGDGRWFVEKSAQYARDRVVFGRPIGQNQGVQFPIAEAHIEIEAADLMRWRAC 306 Query: 303 INKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEI 360 D G+ G A MAK AA+ + E +Q HGG+G+ +Y VER R+ ++ ++ Sbjct: 307 DEYDAGRNAGAAANMAKYLAAKASWEAANACLQTHGGFGFANEYDVERKFRETRLYQV 364 Lambda K H 0.315 0.133 0.373 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: 352 Number of extensions: 15 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: 378 Length of database: 387 Length adjustment: 30 Effective length of query: 348 Effective length of database: 357 Effective search space: 124236 Effective search space used: 124236 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: 42 (22.0 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