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 PP_4201 PP_4201 Electron transfer flavoprotein subunit alpha
Query= BRENDA::D2RIQ3 (340 letters) >FitnessBrowser__Putida:PP_4201 Length = 309 Score = 145 bits (365), Expect = 2e-39 Identities = 92/263 (34%), Positives = 139/263 (52%), Gaps = 10/263 (3%) Query: 68 GADLVYVCQDPAFKYYSTDEYTNAFCEMIDEYQPSSVFIGATNDGRDLGPRIAARVNTGL 127 G V V + A+ + + E+ Y S V AT +G+++ PR+AA ++ Sbjct: 53 GVAKVLVADNAAYAHVLPENVAPLIVELAKGY--SHVLAPATTNGKNILPRVAALLDVDQ 110 Query: 128 CADCTILDAEEDGLIEWTRPAAGGNIMATILCKEHRPQMGTVRPKTFKAMEPDASRTGEV 187 ++ +++ + + RP GN +AT+ ++ TVR F A+ A+ G Sbjct: 111 ISEIISVESADT----FKRPIYAGNAIATVQSSA-AIKVITVRTTGFDAV---AAEGGSA 162 Query: 188 INYTLKNHVDDRVTCIRREEVVSEGEMAIDDAPFVCSGGRGMKAKENFSLLYDLAHALGG 247 + + ++ EE+ + A V SGGRGM +NF LY LA LG Sbjct: 163 AVEAVGAAHNAGISAFVGEELAKSDRPELTAAKIVVSGGRGMGNGDNFKHLYSLADKLGA 222 Query: 248 AVGGSRAAVDEGFIEHPRQVGQSGKTVTPKIYFACGISGSVQHKAGMSKSDTIVCINKDP 307 AVG SRAAVD GF+ + QVGQ+GK V P++Y A GISG++QH AGM S IV INKD Sbjct: 223 AVGASRAAVDAGFVPNDMQVGQTGKIVAPQLYIAVGISGAIQHLAGMKDSKVIVAINKDE 282 Query: 308 DAPMFEISKYGIVGDALKILPLL 330 +AP+F+++ YG+V D + +P L Sbjct: 283 EAPIFQVADYGLVADLFEAVPEL 305 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: 265 Number of extensions: 13 Number of successful extensions: 1 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: 309 Length adjustment: 28 Effective length of query: 312 Effective length of database: 281 Effective search space: 87672 Effective search space used: 87672 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: 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