Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate 7024199 Shewana3_1406 electron transfer flavoprotein, alpha subunit (RefSeq)
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__ANA3:7024199 Length = 308 Score = 166 bits (421), Expect = 5e-46 Identities = 116/322 (36%), Positives = 171/322 (53%), Gaps = 18/322 (5%) Query: 4 VLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTL-AHYGADEVI 62 +LV+ E ++ + +++ A I D V L++G + + A G +V+ Sbjct: 3 ILVLAEHDNAALKLDTAKVVTAACAIGDD----VHVLVVGHQCGAVAQAAQALQGVAQVL 58 Query: 63 VVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCTG 122 V D+ A + E K + A + +L A+S G+D PRV+A + ++ G Sbjct: 59 VADNSAYEAHLAENVAKLLVDL--APNYSHILAAASSAGKDTLPRVAALLDVAQISEVIG 116 Query: 123 LAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRFKV 182 + V+ DT RP + GN +AT+ D M TVR + + A + Sbjct: 117 V-VSSDT----FVRPIYAGNALATVQSHDAIKVM-TVRASAF--DAAAQGNSAAVTTLDK 168 Query: 183 EFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYELAEIIGGEVSGS 242 F + Q V + ++ +A I+VS GRGMG EN +L +LA+ +G V S Sbjct: 169 VF---EAKTQFVSQSLTVSARPELGNAGIIVSGGRGMGSGENFGMLEQLADKLGAAVGAS 225 Query: 243 RATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEAPIF 302 RA +DAG++ QVGQTGK V P+LYIA GISGAIQH+AGM+DA+ IVAINK+PEAPIF Sbjct: 226 RAAVDAGFVPNDLQVGQTGKIVAPNLYIAVGISGAIQHLAGMKDAKVIVAINKDPEAPIF 285 Query: 303 KYADVGIVGDVHKVLPELISQL 324 + AD G+ D+ +PELIS L Sbjct: 286 QVADYGLEADLFDAVPELISTL 307 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: 259 Number of extensions: 6 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: 308 Length adjustment: 28 Effective length of query: 308 Effective length of database: 280 Effective search space: 86240 Effective search space used: 86240 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