Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.109) (characterized)
to candidate Ga0059261_2886 Ga0059261_2886 electron transfer flavoprotein beta subunit
Query= BRENDA::Q18AQ6 (260 letters) >FitnessBrowser__Korea:Ga0059261_2886 Length = 249 Score = 94.4 bits (233), Expect = 2e-24 Identities = 73/215 (33%), Positives = 113/215 (52%), Gaps = 9/215 (4%) Query: 1 MNIVVCIKQVPDTT---EVKLDPNTGTLIRDGVPSIINPDDKAGLEEAIKLKEEMGA-HV 56 M I+V +K+V D VK D TG + + V +NP D+ +EEAI+LKE+ A + Sbjct: 1 MKILVPVKRVLDYNVKPRVKAD-GTGVDLAN-VKMSMNPFDEIAVEEAIRLKEKGAATEI 58 Query: 57 TVITMGPPQADMALKEALAMGADRGILLTDRAFAGADTWATSSALAGALKNIDFDIIIAG 116 V+++G +A L+ ALAMGADR IL+ A + + LA + +II G Sbjct: 59 VVVSIGEQKAQETLRTALAMGADRAILIV--AEDKVEPLGVAKLLAKVAEAEAPGLIILG 116 Query: 117 RQAIDGDTAQVGPQIAEHLNLPSITYAEEIKTEGEYVLVKRQFEDCCHDLKVKMPCLITT 176 +QAID D Q G + L T+A +++ GE V V R+ + +K+K+P ++TT Sbjct: 117 KQAIDDDNNQTGQMLGALLGWGQGTFANKVEIAGEQVDVTREVDGGLETVKLKLPAIVTT 176 Query: 177 LKDMNTPRYMKVGRIYDAFENDVVETWTVKDIEVD 211 +N PRY + I A ++ ++ T D VD Sbjct: 177 DLRLNEPRYASLPNIMKA-KSKPLDQKTPADYGVD 210 Lambda K H 0.316 0.135 0.386 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: 171 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: 260 Length of database: 249 Length adjustment: 24 Effective length of query: 236 Effective length of database: 225 Effective search space: 53100 Effective search space used: 53100 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: 47 (22.7 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