Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate AZOBR_RS05475 AZOBR_RS05475 protein fixB
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__azobra:AZOBR_RS05475 Length = 359 Score = 263 bits (672), Expect = 5e-75 Identities = 136/321 (42%), Positives = 204/321 (63%), Gaps = 4/321 (1%) Query: 4 VLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGS---KVEGLIDTLAHYGADE 60 + V++EQ + +VS EL+G+A ++A +V A++LG+ ++ + YGAD Sbjct: 24 IWVIVEQERGSVHSVSWELVGEARKLADKLGVEVGAVVLGADSPELNAICGDAFTYGADV 83 Query: 61 VIVVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADC 120 V V D LA Y T+PYT+ + + P +VL GAT++GRDLA ++ + TGLTADC Sbjct: 84 VYKVTDPVLADYRTDPYTRVMTDVVNTYKPEIVLLGATTLGRDLAGAIATTLATGLTADC 143 Query: 121 TGLAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRF 180 T L + D + L TRP FGG ++ TI +RPQM+TVRP VM + D+++ + Sbjct: 144 TELDIYMDNRSLAATRPTFGGTLLCTIQTLAYRPQMATVRPRVMSMPDRDDSRTGRVVEV 203 Query: 181 KVEFNDADKLVQVVQVIKEAKK-QVKIEDAKILVSAGRGMGGKENLDILYELAEIIGGEV 239 + D + +V+ I + ++ + ++ A I+V+AG+G+G ENL ++++LA+++GGEV Sbjct: 204 FPNLRETDVITKVLSFIADREQTEAQLAFADIIVAAGKGLGKPENLKLVFDLAKVLGGEV 263 Query: 240 SGSRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEA 299 +R + AGW RQVGQTGKTVRP LYIA GISGAIQH GME ++ I+AIN +P A Sbjct: 264 GVTRPLVQAGWTGFDRQVGQTGKTVRPKLYIAAGISGAIQHRVGMEKSDLILAINTDPNA 323 Query: 300 PIFKYADVGIVGDVHKVLPEL 320 PIF +A +G+VGD +LP L Sbjct: 324 PIFDFAHLGLVGDALTILPAL 344 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: 342 Number of extensions: 10 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: 336 Length of database: 359 Length adjustment: 29 Effective length of query: 307 Effective length of database: 330 Effective search space: 101310 Effective search space used: 101310 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: 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