Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate AO356_21850 AO356_21850 electron transfer flavoprotein subunit beta
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_21850 Length = 311 Score = 146 bits (369), Expect = 6e-40 Identities = 90/228 (39%), Positives = 136/228 (59%), Gaps = 9/228 (3%) Query: 93 VLFGATSIGRDLAPRVSARIHTGLTADCTGLAVAEDTKLLLMTRPAFGGNIMATIVCKDF 152 V+ A+S+GR++ PR++A + G+ +D T + V+ DT RP + GN +AT+ D Sbjct: 89 VVADASSMGRNVLPRIAASLDVGMLSDVTQI-VSTDT----FQRPIYAGNAIATVQSLD- 142 Query: 153 RPQMSTVRPGVMKKNEPDETKEAVINRFKVEFNDADKLVQVVQVIKEAKKQVKIEDAKIL 212 ++ TVR + E + V+ VE + V+ V A ++ + A+++ Sbjct: 143 PIKLLTVRASAFAQALSHEHRCEVV---VVEGGQSASNVRFVSEQLTASERPDLSSARVV 199 Query: 213 VSAGRGMGGKENLDILYELAEIIGGEVSGSRATIDAGWLDKARQVGQTGKTVRPDLYIAC 272 VS GRGM GKE+ ++ +A+ +GG V SRA +D+G+ QVGQTGK V P+LYIA Sbjct: 200 VSGGRGMQGKEHFALIERVADKLGGAVGASRAAVDSGFAPNDLQVGQTGKIVAPELYIAA 259 Query: 273 GISGAIQHIAGMEDAEFIVAINKNPEAPIFKYADVGIVGDVHKVLPEL 320 GISGAIQH+AGM ++ IVAIN++ EAPI + AD V D+ + LP L Sbjct: 260 GISGAIQHLAGMSGSKVIVAINQDAEAPIAQVADYMWVADLFEALPAL 307 Lambda K H 0.316 0.135 0.371 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: 220 Number of extensions: 12 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: 336 Length of database: 311 Length adjustment: 28 Effective length of query: 308 Effective length of database: 283 Effective search space: 87164 Effective search space used: 87164 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: 48 (23.1 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