Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate 5210235 Shew_2678 electron transfer flavoprotein, alpha subunit (RefSeq)
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__PV4:5210235 Length = 313 Score = 131 bits (329), Expect = 3e-35 Identities = 99/296 (33%), Positives = 152/296 (51%), Gaps = 21/296 (7%) Query: 36 KVSALLLGSKVEGLIDTLAHYGADEVIVVDDEALAVYTTEPYTKAAYEAIKAAD-PIVVL 94 KVSA ++GS+ + I T YGA V + ++A A E Y +AI D P +VL Sbjct: 30 KVSAFIIGSEAD--IATAYSYGATHVYYLGNKADA-QMVEDYAATMSQAINDGDKPTLVL 86 Query: 95 FGATSIGRDLAPRVSARIHTGLTADCTGLAVAEDTKLLLMTRPAFGGNIMATIVCKDFRP 154 AT + LA ++S ++ GL D T +++ E M +GG + T Sbjct: 87 LPATKRCKALAAKLSVQLEAGLINDATEVSLDEGVTAKHMV---YGGLAIGTERITS-PV 142 Query: 155 QMSTVRPGVMKKNEPDE--TKEAVINRFKVEFNDADKLVQVVQVIKEAKKQ---VKIEDA 209 + T+ G + D T E V F Q ++ I+ KQ V + A Sbjct: 143 ALVTLASGAFEPQAADTSLTGEGVSLAFVAP-------KQAIRCIERRVKQGNSVDLGKA 195 Query: 210 KILVSAGRGMGGKENLDILYELAEIIGGEVSGSRATIDAG-WLDKARQVGQTGKTVRPDL 268 K +++ G G+G +NL + ELA I E+ SR + W+++ R VG +G ++PD+ Sbjct: 196 KRVIAVGSGIGNLDNLALAGELATAIQAELGCSRPIAETEKWMERERYVGVSGVMLKPDI 255 Query: 269 YIACGISGAIQHIAGMEDAEFIVAINKNPEAPIFKYADVGIVGDVHKVLPELISQL 324 Y+A GISG IQH+ G ++ I+A+NK+ APIF+Y D G+VGD++KVLP LI + Sbjct: 256 YLALGISGQIQHMVGALGSQTILAVNKDKNAPIFQYVDYGLVGDINKVLPALIQAM 311 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: 230 Number of extensions: 8 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: 313 Length adjustment: 28 Effective length of query: 308 Effective length of database: 285 Effective search space: 87780 Effective search space used: 87780 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