Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (subunit 1/2) (EC 1.3.8.1) (characterized)
to candidate Pf6N2E2_1146 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1146 Length = 375 Score = 359 bits (921), Expect = e-104 Identities = 179/372 (48%), Positives = 254/372 (68%) Query: 6 TEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGLD 65 TE+Q I+DMA +FAE+ L P E D+ H + R+ ID+M E GF G+ PE++GG Sbjct: 4 TEEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTG 63 Query: 66 VLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFGL 125 L+Y + +EE++ D +S + S+ PI FG +EQK K+L P+A G +GAF L Sbjct: 64 YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123 Query: 126 TEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAFI 185 TEP AG+DAS+ +T A L+GD Y+LNG K FIT+G+ A +VFA+TD S G GISAFI Sbjct: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 Query: 186 LEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRIG 245 + PG+ ++EDK+G H S T +++FED +VP N LG+EGEG+KIA+ L+GGR+G Sbjct: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRVG 243 Query: 246 VAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAML 305 +AAQA+G+A A AA Y++ER FG+ I + QA+ F +ADMAT+I AR +V++AA L Sbjct: 244 IAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 Query: 306 KNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEGT 365 ++ G+P A+MAK FAS++A +V + A+Q GGYGY D+P ER R+ ++ QIYEGT Sbjct: 304 RDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGT 363 Query: 366 NQVMRIVTSRAL 377 + + R+V SR L Sbjct: 364 SDIQRMVISRNL 375 Lambda K H 0.318 0.134 0.379 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: 369 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: 383 Length of database: 375 Length adjustment: 30 Effective length of query: 353 Effective length of database: 345 Effective search space: 121785 Effective search space used: 121785 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: 50 (23.9 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