Alignments for a candidate for Psest_0084 in Pseudomonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Pseudomonas stutzeri A1501

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate WP_011915126.1 PST_RS20545 C4-dicarboxylate ABC transporter

Query= reanno::psRCH2:GFF84
         (674 letters)



>NCBI__GCF_000013785.1:WP_011915126.1
          Length = 674

 Score = 1296 bits (3353), Expect = 0.0
 Identities = 651/674 (96%), Positives = 662/674 (98%)

Query: 1   MSESQGLHASPSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYP 60
           MSESQGLHASPSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYP
Sbjct: 1   MSESQGLHASPSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYP 60

Query: 61  ARGNGKPFQPVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAAR 120
           ARGNGKPFQPVAWLLGLAGFATF YQWYFEADLIQRSGDMT+ DMVVGLTLIVLVFEAAR
Sbjct: 61  ARGNGKPFQPVAWLLGLAGFATFIYQWYFEADLIQRSGDMTSTDMVVGLTLIVLVFEAAR 120

Query: 121 RVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATY 180
           RVMGIALPIIC LFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATY
Sbjct: 121 RVMGIALPIICGLFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATY 180

Query: 181 IFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTT 240
           IFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTT
Sbjct: 181 IFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTT 240

Query: 241 GQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALI 300
           GQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALI
Sbjct: 241 GQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALI 300

Query: 301 PALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTP 360
           PALLYFGSVFWMVHLEAKRAGLKGLPKDECPSA AAVKERWYLLIPL+VLVWLLFSGRTP
Sbjct: 301 PALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAWAAVKERWYLLIPLLVLVWLLFSGRTP 360

Query: 361 MFAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALV 420
           MFAGTIGLALTAIVILGSAIILKVS+F LRIAFWIALGLLCAGFFQLGIGVIFGVIAALV
Sbjct: 361 MFAGTIGLALTAIVILGSAIILKVSSFGLRIAFWIALGLLCAGFFQLGIGVIFGVIAALV 420

Query: 421 AVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAV 480
           AVCWFIKGGRDTL ICLHALVEGARHAVPVGIACALVGVIIG+VSLTGVASTFAGYILAV
Sbjct: 421 AVCWFIKGGRDTLTICLHALVEGARHAVPVGIACALVGVIIGIVSLTGVASTFAGYILAV 480

Query: 481 GENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIM 540
           GENNLFLSL+LTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIM
Sbjct: 481 GENNLFLSLILTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIM 540

Query: 541 ADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATL 600
           ADLTPPVALACFAAAPIAKE+GLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATL
Sbjct: 541 ADLTPPVALACFAAAPIAKEKGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATL 600

Query: 601 YMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFLI 660
           YMLFKAAFA+GLWGAVFTGYLQRPMALWEKVL F A A+M+LA P+SDEIGFALGA+FL 
Sbjct: 601 YMLFKAAFAIGLWGAVFTGYLQRPMALWEKVLGFVAGAAMILATPMSDEIGFALGAIFLA 660

Query: 661 QHIWRARRAEPATA 674
           QHIWRARRAEPA A
Sbjct: 661 QHIWRARRAEPAAA 674


Lambda     K      H
   0.330    0.143    0.445 

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: 1833
Number of extensions: 81
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: 674
Length of database: 674
Length adjustment: 39
Effective length of query: 635
Effective length of database: 635
Effective search space:   403225
Effective search space used:   403225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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