Aligments for a candidate for malE in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Aligments for a candidate for malE in Pseudomonas stutzeri RCH2

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate GFF849 Psest_0863 Maltose-binding periplasmic proteins/domains

Query= reanno::psRCH2:GFF849
         (395 letters)



>lcl|FitnessBrowser__psRCH2:GFF849 Psest_0863 Maltose-binding
           periplasmic proteins/domains
          Length = 395

 Score =  801 bits (2069), Expect = 0.0
 Identities = 395/395 (100%), Positives = 395/395 (100%)

Query: 1   MNKKFWCIATVGLAATFSLPLPALAAIEEGKLVVWINGDKGYKGLAEVGKKFTAETGIPV 60
           MNKKFWCIATVGLAATFSLPLPALAAIEEGKLVVWINGDKGYKGLAEVGKKFTAETGIPV
Sbjct: 1   MNKKFWCIATVGLAATFSLPLPALAAIEEGKLVVWINGDKGYKGLAEVGKKFTAETGIPV 60

Query: 61  EVAHPDSATDKFQQAAATGNGPDIFIWAHDRIGEWAKSGLLTPVTPSADTKSGIADFSWQ 120
           EVAHPDSATDKFQQAAATGNGPDIFIWAHDRIGEWAKSGLLTPVTPSADTKSGIADFSWQ
Sbjct: 61  EVAHPDSATDKFQQAAATGNGPDIFIWAHDRIGEWAKSGLLTPVTPSADTKSGIADFSWQ 120

Query: 121 AVTYDNKLWGYPISVETIGLIYNKALVDTPPKTFDDVMALNEKLAAQGKRAILWDYNNTY 180
           AVTYDNKLWGYPISVETIGLIYNKALVDTPPKTFDDVMALNEKLAAQGKRAILWDYNNTY
Sbjct: 121 AVTYDNKLWGYPISVETIGLIYNKALVDTPPKTFDDVMALNEKLAAQGKRAILWDYNNTY 180

Query: 181 FTWPLLSAKGGYVFEHADGGYDVKSTGVNNAGAKAGAQVLRDLIDKGVMPKGADYSVAEA 240
           FTWPLLSAKGGYVFEHADGGYDVKSTGVNNAGAKAGAQVLRDLIDKGVMPKGADYSVAEA
Sbjct: 181 FTWPLLSAKGGYVFEHADGGYDVKSTGVNNAGAKAGAQVLRDLIDKGVMPKGADYSVAEA 240

Query: 241 AFNKGDSAMMISGPWAWSNIEKSGIDFGVAPIPAIDGEPGKPFVGVAAALLNAASPNKDL 300
           AFNKGDSAMMISGPWAWSNIEKSGIDFGVAPIPAIDGEPGKPFVGVAAALLNAASPNKDL
Sbjct: 241 AFNKGDSAMMISGPWAWSNIEKSGIDFGVAPIPAIDGEPGKPFVGVAAALLNAASPNKDL 300

Query: 301 AVEFLENYLLQVEGLKTVNADVPLGAVANTAYMEELSANPHIKATFENAQMGEPMPNVPE 360
           AVEFLENYLLQVEGLKTVNADVPLGAVANTAYMEELSANPHIKATFENAQMGEPMPNVPE
Sbjct: 301 AVEFLENYLLQVEGLKTVNADVPLGAVANTAYMEELSANPHIKATFENAQMGEPMPNVPE 360

Query: 361 MGAFWSSMAAALTNITSGRQDVDAALDDAAKRITR 395
           MGAFWSSMAAALTNITSGRQDVDAALDDAAKRITR
Sbjct: 361 MGAFWSSMAAALTNITSGRQDVDAALDDAAKRITR 395


Lambda     K      H
   0.315    0.132    0.401 

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: 827
Number of extensions: 31
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: 395
Length of database: 395
Length adjustment: 31
Effective length of query: 364
Effective length of database: 364
Effective search space:   132496
Effective search space used:   132496
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources