Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_011385957.1 AMB_RS18215 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2397 (379 letters) >NCBI__GCF_000009985.1:WP_011385957.1 Length = 378 Score = 545 bits (1404), Expect = e-160 Identities = 268/375 (71%), Positives = 315/375 (84%) Query: 1 MLPNEDQNAIAEMARQFAQERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGS 60 M+ E+Q I +MAR FA+E+L P A +W REH +P +AI EM LGF GM+VP +W G+ Sbjct: 1 MIATEEQQLIRDMARSFAREKLAPNAARWDREHLFPTDAIAEMGELGFLGMVVPSEWDGA 60 Query: 61 DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKSDFLTPLARGEQIGA 120 T Y++YAMA+ EIAAG G STIMSVHNSVGC+PIL +G E QK +FL P+ARGE++G Sbjct: 61 GTDYVSYAMAVMEIAAGCGPLSTIMSVHNSVGCMPILTYGTEAQKDEFLRPMARGEKLGC 120 Query: 121 FALTEPQAGSDASSLRTRARRDGDHYVLNGAKQFITSGKHAGTVIVFAVTDPDAGKGGIS 180 F LTEP+AGSDA+S+RTRARRDGDHYVL+GAKQFI++ K+ IVFAVTDP AGK GIS Sbjct: 121 FCLTEPEAGSDAASIRTRARRDGDHYVLSGAKQFISTAKNGQVAIVFAVTDPQAGKRGIS 180 Query: 181 AFIVPTDSPGYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGG 240 AF+VPTD+PG+ VVRVEDKLGQH SDTCQ+AFED+RVP + RLGEEG+G +IALANLEGG Sbjct: 181 AFVVPTDTPGFTVVRVEDKLGQHLSDTCQLAFEDMRVPASRRLGEEGDGLKIALANLEGG 240 Query: 241 RIGIAAQAVGMARAAFEAARDYARDRETFGKPIIEHQAVAFRLADMATQIAVARQMVHHA 300 R+GIAAQ+VGMAR+A + A YA++R+ FGKPI EHQAVAFRLADMAT++ VA QMV HA Sbjct: 241 RLGIAAQSVGMARSALDHALAYAKERKQFGKPIFEHQAVAFRLADMATRVEVAEQMVLHA 300 Query: 301 AALREVGRPALVEASMAKLFASEMAEKVCSAAIQTLGGYGYLADFPVERIYRDVRVCQIY 360 A+LR+ G P L EASMAKLFASEMAE+VCS AIQ GGYGYLADFPVERIYRDVRVCQIY Sbjct: 301 ASLRDAGLPCLKEASMAKLFASEMAERVCSDAIQIHGGYGYLADFPVERIYRDVRVCQIY 360 Query: 361 EGTSDIQRLVISRNL 375 EGTSDIQRLVISR L Sbjct: 361 EGTSDIQRLVISRAL 375 Lambda K H 0.320 0.135 0.391 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: 499 Number of extensions: 15 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: 379 Length of database: 378 Length adjustment: 30 Effective length of query: 349 Effective length of database: 348 Effective search space: 121452 Effective search space used: 121452 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 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