Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_011913061.1 PST_RS09700 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >NCBI__GCF_000013785.1:WP_011913061.1 Length = 379 Score = 652 bits (1681), Expect = 0.0 Identities = 322/375 (85%), Positives = 351/375 (93%) Query: 1 MLPTDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGC 60 MLP ++Q I++ ARQFA+ERLKPFA +W REHR+P EAIGEMA LGFFGMLVPEQWGG Sbjct: 1 MLPNEDQCAIAEMARQFARERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGS 60 Query: 61 DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGA 120 DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPIL+FGND QK FL PLA G +GA Sbjct: 61 DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNDQQKRDFLGPLARGEQIGA 120 Query: 121 FALTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGIS 180 FALTEPQAGSDASSL+TRAR +GDHYVLNG KQFITSG++AG VIVFAVTDP AGKRGIS Sbjct: 121 FALTEPQAGSDASSLRTRARRDGDHYVLNGAKQFITSGKHAGTVIVFAVTDPDAGKRGIS 180 Query: 181 AFIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGG 240 AFIVPTDSPGY+V RVEDKLGQHASDTCQI FED++VPVANRLGEEGEGY+IALANLEGG Sbjct: 181 AFIVPTDSPGYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGG 240 Query: 241 RVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300 R+GIA+Q+VGMARAAFEAARDYA ERE+FGKPIIEHQAVAFRLADMATQIAVARQMVH+A Sbjct: 241 RIGIAAQAVGMARAAFEAARDYAGERETFGKPIIEHQAVAFRLADMATQIAVARQMVHHA 300 Query: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIY 360 AALR++G+PALVEASMAKLFASEMAE+VCS A+QTLGGYGYLSDFP+ERIYRDVRVCQIY Sbjct: 301 AALREAGRPALVEASMAKLFASEMAERVCSAAIQTLGGYGYLSDFPVERIYRDVRVCQIY 360 Query: 361 EGTSDIQRMVISRNL 375 EGTSDIQR+VISRNL Sbjct: 361 EGTSDIQRLVISRNL 375 Lambda K H 0.319 0.134 0.389 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: 552 Number of extensions: 11 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: 375 Length of database: 379 Length adjustment: 30 Effective length of query: 345 Effective length of database: 349 Effective search space: 120405 Effective search space used: 120405 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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