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_084199172.1 C0029_RS09065 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >NCBI__GCF_002869505.1:WP_084199172.1 Length = 378 Score = 273 bits (699), Expect = 4e-78 Identities = 150/377 (39%), Positives = 228/377 (60%), Gaps = 3/377 (0%) Query: 3 LNSKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEG 62 +++++ + +++ E E++P +E+ P E + AG++ P+ YGG G Sbjct: 1 MDNEELTLFRDMARRAYEQEIEPHYEGWEEQHLVPRELWNTLGAAGLLCPDMPEAYGGAG 60 Query: 63 GDTVGYIMAVEELSRVCGTTGVI--LSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLG 120 + +EE+SR+ G G+ H+++ + I +G EEQKQ++L + +GE +G Sbjct: 61 TSPRVCLAMIEEMSRM-GFGGLASGYGIHSNIVAPYINHFGTEEQKQQWLPKMITGEAVG 119 Query: 121 AFGLTEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGI 180 A +TEP AG+D G +TTAV DG+E++LNGSKIFITN I D+ +V A+TD KG KG Sbjct: 120 ALAMTEPGAGSDVQGIRTTAVRDGEEWVLNGSKIFITNGIHADLVIVAAITDPGKGAKGT 179 Query: 181 SAFIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDG 240 S F+V+ PGF G K +K+G S T+EL F+D R+P LLG+E +GF I M+ L Sbjct: 180 SLFLVDASLPGFEKGNKIEKIGQHASDTAELFFQDVRLPASALLGEENKGFVIMMTELPR 239 Query: 241 GRIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQ 300 R+GIAAQA+ A+GA+D TV YV ER FG+ ++ FQNT+F LA+++ ++ R L + Sbjct: 240 ERLGIAAQAVAAAEGAMDITVDYVLERKAFGQTVASFQNTRFTLAEVKTEIALNRALYEK 299 Query: 301 AAINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEI 360 A + G+ +AAM K E + +QL GGYGYT +YP+ R DA+I I Sbjct: 300 CADDYARGELTADDAAMLKYANTEMQCSTIDQCLQLFGGYGYTAEYPISRYYTDARIQRI 359 Query: 361 YEGTSEVQRMVISGKLL 377 Y GTSE+ R +++ +L Sbjct: 360 YGGTSEIMRELVARSIL 376 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: 390 Number of extensions: 23 Number of successful extensions: 2 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: 378 Length adjustment: 30 Effective length of query: 348 Effective length of database: 348 Effective search space: 121104 Effective search space used: 121104 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 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