Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.109) (characterized)
to candidate 351332 BT1804 electron transfer flavoprotein beta-subunit (NCBI ptt file)
Query= BRENDA::Q18AQ6 (260 letters) >FitnessBrowser__Btheta:351332 Length = 290 Score = 170 bits (430), Expect = 4e-47 Identities = 115/271 (42%), Positives = 151/271 (55%), Gaps = 29/271 (10%) Query: 1 MNIVVCIKQVPDTTEVKLDPNT--GTLIRDGVPSIINPDDKAGLEEAIKLKE-EMGAHVT 57 + IVV KQVPDT V D GT+ R +P+I NP+D LE+A++LK+ G+ VT Sbjct: 3 LKIVVLAKQVPDTRNVGKDAMKADGTINRAALPAIFNPEDLNALEQALRLKDAHPGSTVT 62 Query: 58 VITMGPPQADMALKEALAMGADRGILLTDRAFAGADTWATSSALAGALKNI-DFDIIIAG 116 ++TMGP +A ++E L GAD G LLTDRAFAGADT ATS ALA A++ I + DIII G Sbjct: 63 ILTMGPGRAADIIREGLFRGADNGYLLTDRAFAGADTLATSYALATAIRKIGECDIIIGG 122 Query: 117 RQAIDGDTAQVGPQIAEHLNLPSITYAEEIKTEGE-YVLVKRQFEDCCHDLKVKMPCLIT 175 RQAIDGDTAQVGPQ+AE L L ITYAEEI G+ + VKR + ++ +P +IT Sbjct: 123 RQAIDGDTAQVGPQVAEKLGLTQITYAEEILEVGDGKIKVKRHIDGGVETVEGPLPIVIT 182 Query: 176 T-----------------LKDMNTPRYMKVGR-----IYDAFENDVVETWTVKDIEVDPS 213 K T + G +YD + + W+V D+ D + Sbjct: 183 VNGSAAPCRPRNAKLVQKYKHAKTVTEKQQGNLDYTDLYDKRDYLNLPEWSVADVNGDLA 242 Query: 214 NLGLKGSPTSV--FKSFTKSVKPAGTIYNED 242 GL GSPT V ++ K + TI D Sbjct: 243 QCGLSGSPTKVKAIQNIVFQAKESKTISGSD 273 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: 212 Number of extensions: 11 Number of successful extensions: 5 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: 290 Length adjustment: 25 Effective length of query: 235 Effective length of database: 265 Effective search space: 62275 Effective search space used: 62275 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