GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acdH in Marinobacter adhaerens HP15

Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate GFF1029 HP15_1008 acyl-CoA dehydrogenase domain protein

Query= reanno::acidovorax_3H11:Ac3H11_2996
         (376 letters)



>lcl|FitnessBrowser__Marino:GFF1029 HP15_1008 acyl-CoA dehydrogenase
           domain protein
          Length = 383

 Score =  261 bits (667), Expect = 2e-74
 Identities = 149/379 (39%), Positives = 212/379 (55%), Gaps = 4/379 (1%)

Query: 1   MLLTQDQE---MIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEF 57
           M ++ D+E   M RD+V    + E+ PH   W+K    P++    L   G   + VPEE+
Sbjct: 1   MTVSVDKEELAMFRDSVIKVLEKEVTPHYEAWEKSGLVPRELWNTLGNAGMLCVDVPEEW 60

Query: 58  GGANLDYLTLALVLEEIAA-GDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGE 116
           GG    +    +V EE+A  G G  ST + V +  V   L   GN +Q++ WL  L  GE
Sbjct: 61  GGIGAPFQFSVVVGEELARMGFGALSTNVMVHSDIVAPYLSHMGNEEQRQQWLPKLVSGE 120

Query: 117 MLGAFCLTEPHVGSDASALRTTAVKQGDEYVINGVKQFITSGKNGQVAIVIAVTDKGAGK 176
            +GA  +TEP  GSD  A+RT+AVK GDEY++NG K FIT+G++  + IV A TD  AG 
Sbjct: 121 AVGAIAMTEPGAGSDLQAIRTSAVKDGDEYILNGSKTFITNGQHADMVIVAAKTDPKAGA 180

Query: 177 KGMSAFLVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIALGA 236
           +G+S FLV T+ PG+   R  DK+GQHS DT+++ F + RIPA  L+G EG+G+   +  
Sbjct: 181 RGISLFLVDTSLPGFSKGRNLDKIGQHSGDTSELFFSDMRIPASALLGEEGQGFVYLMKE 240

Query: 237 LEGGRIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAARQL 296
           L   R+ I A  V  AR + D  +AY++ERE FG  +   Q   F +A   T     +  
Sbjct: 241 LPRERLVIGALGVAAARGSLDLTIAYAQERELFGQKLAQLQNTRFEIARMETDYRVNKAF 300

Query: 297 IWHAAALRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDVRV 356
           +       D G+     A+MAK  A+EM  RV    +Q  GGYG   ++P+ R + D RV
Sbjct: 301 VDQCIDQYDLGELDAPTASMAKYSATEMQCRVADGCLQLFGGYGYTTEYPISRAFIDARV 360

Query: 357 CQIYEGTSDVQKIIIQRAL 375
            +IY GTS+V K II R++
Sbjct: 361 QRIYGGTSEVMKEIIARSV 379


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: 348
Number of extensions: 9
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: 376
Length of database: 383
Length adjustment: 30
Effective length of query: 346
Effective length of database: 353
Effective search space:   122138
Effective search space used:   122138
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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