Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate WP_050465593.1 AKL27_RS24925 acyl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >NCBI__GCF_001189915.1:WP_050465593.1 Length = 376 Score = 486 bits (1252), Expect = e-142 Identities = 246/375 (65%), Positives = 293/375 (78%) Query: 1 MLLTQDQEMIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEFGGA 60 M+ +QEMIRD +R FA+ +L P+AA W+ FP++A Q L LGA G+ V EE+GG Sbjct: 1 MIPNTEQEMIRDTIRSFAREQLLPNAAAWEAGGIFPREALQELGRLGALGVTVSEEYGGT 60 Query: 61 NLDYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEMLGA 120 LDY TLA VLEEIAAG G TST +SV N V I ++G+ QK+ +LT A GE+LG Sbjct: 61 GLDYATLAFVLEEIAAGHGATSTIVSVQNSLVCGITEKFGSHAQKKRYLTGFATGELLGC 120 Query: 121 FCLTEPHVGSDASALRTTAVKQGDEYVINGVKQFITSGKNGQVAIVIAVTDKGAGKKGMS 180 FCLTEPH GSDASALRTTA + G +V+NGVKQFIT+G VA+VIAVTDK GKKGMS Sbjct: 121 FCLTEPHTGSDASALRTTARRDGGGWVLNGVKQFITTGSEADVAVVIAVTDKDKGKKGMS 180 Query: 181 AFLVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIALGALEGG 240 FLVPT++PGY V +E KLGQH+SDTAQI FD CR+ + L+GAEGEGYKIAL LE G Sbjct: 181 CFLVPTDSPGYCVTGIEKKLGQHASDTAQITFDQCRVDGDALVGAEGEGYKIALSNLEAG 240 Query: 241 RIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAARQLIWHA 300 RIGIAAQSVGMAR+A++ AL Y++ERESFG + HQAV FRLAD AT IEAARQL+ HA Sbjct: 241 RIGIAAQSVGMARAAYEVALDYARERESFGQPLTAHQAVAFRLADMATTIEAARQLLHHA 300 Query: 301 AALRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDVRVCQIY 360 AAL+DAG PCLKEA+MAKLFASE AE+VCSAA+QTLGGYG DF +ERIYRDVRV QIY Sbjct: 301 AALKDAGLPCLKEASMAKLFASEGAEKVCSAALQTLGGYGYTQDFAIERIYRDVRVTQIY 360 Query: 361 EGTSDVQKIIIQRAL 375 EGTSD+Q+++I RA+ Sbjct: 361 EGTSDIQRMVIARAI 375 Lambda K H 0.319 0.134 0.396 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: 479 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: 376 Length of database: 376 Length adjustment: 30 Effective length of query: 346 Effective length of database: 346 Effective search space: 119716 Effective search space used: 119716 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 24 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