Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate PP_3725 PP_3725 putative Acyl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >FitnessBrowser__Putida:PP_3725 Length = 386 Score = 267 bits (683), Expect = 3e-76 Identities = 161/381 (42%), Positives = 227/381 (59%), Gaps = 13/381 (3%) Query: 3 LTQDQEMIRDAVRDFAQTELWPHAARWDKEHHF-PKDAHQ--GLA-ALGAYGICVPEEFG 58 LTQ+QEM+ +AVR F EL PH D+ P+ A Q G A A G Y +PEE G Sbjct: 5 LTQEQEMLVEAVRSFVAKELLPHEEAVDRADAVSPELAAQIRGKAIAAGFYAFNMPEEVG 64 Query: 59 GANLDYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEML 118 G LDYL+ AL+ E++ S A+ V + ILM + +Q D+L P +GE + Sbjct: 65 GGGLDYLSQALIERELSK----VSWALHVFVARPSKILMACKD-EQINDYLLPCVQGEKV 119 Query: 119 GAFCLTEPHVGSDASALRTTAVKQGDEYVINGVKQFITSGKNGQVAIVIAVTD----KGA 174 F LTEP GSDA+A++T AV+QGD++VING K FI+ + AIV AVTD G Sbjct: 120 DCFALTEPGAGSDANAIKTRAVRQGDDFVINGSKHFISHAGHADFAIVFAVTDTYEHNGR 179 Query: 175 GKKGMSAFLVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIAL 234 + ++A LV PG + R + T ++ FD+CR+PA ++G G+G+++A Sbjct: 180 KRNAVTALLVDRGTPGMTIRRGPKCVSNRGYHTYELFFDDCRVPASKVLGEVGKGWEVAN 239 Query: 235 GALEGGRIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAAR 294 L GR+ +AA VG A+ A D +L ++ +R+ FG AI ++Q V F+LAD ATQI AA Sbjct: 240 AWLTAGRVMVAANCVGQAQRALDLSLQWAADRKQFGQAIGSYQGVSFKLADMATQIRAAE 299 Query: 295 QLIWHAAALRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDV 354 L H A D G EA MAKLFASE+ +V A+Q GG G++++ PVERI+R+ Sbjct: 300 MLTLHTAWKMDQGNMTDGEAGMAKLFASEVLGKVADEAVQIFGGMGLMDEGPVERIWRNA 359 Query: 355 RVCQIYEGTSDVQKIIIQRAL 375 R+ +I+EGTS++Q+ II R L Sbjct: 360 RIERIWEGTSEIQRHIIAREL 380 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: 356 Number of extensions: 18 Number of successful extensions: 4 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: 386 Length adjustment: 30 Effective length of query: 346 Effective length of database: 356 Effective search space: 123176 Effective search space used: 123176 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