Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate SMa0819 SMa0819 FixB electron transfer flavoprotein alpha chain
Query= BRENDA::D2RIQ3 (340 letters) >FitnessBrowser__Smeli:SMa0819 Length = 353 Score = 229 bits (583), Expect = 1e-64 Identities = 129/324 (39%), Positives = 185/324 (57%), Gaps = 5/324 (1%) Query: 13 KDLWVYVEHYKGEPVHVVYELLGECRKLADKCNQKLAAVLITDDAKDVPSKLIAR----G 68 +++WV++E G+ V ELLGE RKLADK LA V+I + IA G Sbjct: 13 RNVWVFIELEHGQVHPVSIELLGEGRKLADKLGVHLAGVVIGPPGGQGTANAIADAFAYG 72 Query: 69 ADLVYVCQDPAFKYYSTDEYTNAFCEMIDEYQPSSVFIGATNDGRDLGPRIAARVNTGLC 128 ADL Y+ + P +Y + +T A +++ +P + +GAT GRDL +A + TGL Sbjct: 73 ADLSYLVESPLLAHYRNEPFTKALTDLVLANKPEILLLGATTLGRDLAGSVATTLKTGLT 132 Query: 129 ADCTILDAEEDGLIEWTRPAAGGNIMATILCKEHRPQMGTVRPKTFKAMEPDASRTGEVI 188 ADCT L+ + DG + TRP GG+++ TI + RPQM TVRP + TG +I Sbjct: 133 ADCTELNVDSDGSLAATRPTFGGSLLCTIYTLKCRPQMATVRPSVMATPQRVNRPTGSII 192 Query: 189 NYTLKNHVDDRVTCIRREEVVSEGEMA-IDDAPFVCSGGRGMKAKENFSLLYDLAHALGG 247 + LK ++ T + + +A + A V +GG G+ A +N LL DLA LGG Sbjct: 193 RHDLKMLEEEIATKVLAFFSDCDSTIANLAYADVVVAGGLGLGAVQNLQLLKDLARTLGG 252 Query: 248 AVGGSRAAVDEGFIEHPRQVGQSGKTVTPKIYFACGISGSVQHKAGMSKSDTIVCINKDP 307 G SR V +G++ RQ+GQ+G T+ PK+Y A GISG+VQH+ G+ SD IV IN DP Sbjct: 253 DFGCSRPLVQKGWMPFDRQIGQTGNTIRPKLYIAAGISGAVQHRVGVEGSDLIVAINTDP 312 Query: 308 DAPMFEISKYGIVGDALKILPLLT 331 +AP+F+ + G+V DA+ LP LT Sbjct: 313 NAPIFDFAHLGVVADAISFLPALT 336 Lambda K H 0.318 0.136 0.406 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: 307 Number of extensions: 18 Number of successful extensions: 3 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: 340 Length of database: 353 Length adjustment: 29 Effective length of query: 311 Effective length of database: 324 Effective search space: 100764 Effective search space used: 100764 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 (21.7 bits) S2: 49 (23.5 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