Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate Pf1N1B4_5613 Electron transfer flavoprotein, alpha subunit
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5613 Length = 318 Score = 153 bits (387), Expect = 5e-42 Identities = 109/313 (34%), Positives = 162/313 (51%), Gaps = 14/313 (4%) Query: 10 QRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHYGADEVIVVDDEAL 69 Q V+ +L + A +I D V+ +GS E G +V+V D+ A Sbjct: 14 QDNKVLAPATLNTVAAAAKIGGDIHVLVAGAFVGSVAEAAAKIA---GVAKVLVADNAAY 70 Query: 70 AVYTTEPYTKAAYEAIKAADPIV--VLFGATSIGRDLAPRVSARIHTGLTADCTGLAVAE 127 A E + I VL ATS G+++ PRV+A++ ++ + A+ Sbjct: 71 AYQLPENVAPLVAGLVIEQRTIYSHVLASATSNGKNILPRVAAQLDADQISEIISVESAD 130 Query: 128 DTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRFKVEFNDA 187 K RP + GN +AT+ + ++ TVR + AV +DA Sbjct: 131 TFK-----RPIYAGNAIATVQ-SNAAVKVITVRATGFDPVAAEGGSAAV--EAVAAAHDA 182 Query: 188 DKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYELAEIIGGEVSGSRATID 247 V + + ++ + ++ AKI+VS GRGM +N LY LA+ +G V SRA +D Sbjct: 183 GISTFVGEELAKSDRP-ELTAAKIVVSGGRGMQNGDNFKHLYALADKLGAAVGASRAAVD 241 Query: 248 AGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEAPIFKYADV 307 AG++ QVGQTGK V P LYIA GISGAIQH+AGM+D++ IVAINK+ EAPIF+ AD Sbjct: 242 AGFVPNDMQVGQTGKIVAPQLYIAVGISGAIQHLAGMKDSKVIVAINKDEEAPIFQVADY 301 Query: 308 GIVGDVHKVLPEL 320 G+V D+ + +PE+ Sbjct: 302 GLVADLFEAIPEM 314 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: 272 Number of extensions: 9 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: 318 Length adjustment: 28 Effective length of query: 308 Effective length of database: 290 Effective search space: 89320 Effective search space used: 89320 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