GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Psest_0084 in Pseudomonas stutzeri RCH2

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate GFF84 Psest_0084 TRAP transporter, 4TM/12TM fusion protein

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



>FitnessBrowser__psRCH2:GFF84
          Length = 674

 Score = 1328 bits (3437), Expect = 0.0
 Identities = 674/674 (100%), Positives = 674/674 (100%)

Query: 1   MSESQGLHASPSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYP 60
           MSESQGLHASPSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYP
Sbjct: 1   MSESQGLHASPSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYP 60

Query: 61  ARGNGKPFQPVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAAR 120
           ARGNGKPFQPVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAAR
Sbjct: 61  ARGNGKPFQPVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAAR 120

Query: 121 RVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATY 180
           RVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATY
Sbjct: 121 RVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATY 180

Query: 181 IFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTT 240
           IFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTT
Sbjct: 181 IFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTT 240

Query: 241 GQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALI 300
           GQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALI
Sbjct: 241 GQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALI 300

Query: 301 PALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTP 360
           PALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTP
Sbjct: 301 PALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTP 360

Query: 361 MFAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALV 420
           MFAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALV
Sbjct: 361 MFAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALV 420

Query: 421 AVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAV 480
           AVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAV
Sbjct: 421 AVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAV 480

Query: 481 GENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIM 540
           GENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIM
Sbjct: 481 GENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIM 540

Query: 541 ADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATL 600
           ADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATL
Sbjct: 541 ADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATL 600

Query: 601 YMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFLI 660
           YMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFLI
Sbjct: 601 YMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFLI 660

Query: 661 QHIWRARRAEPATA 674
           QHIWRARRAEPATA
Sbjct: 661 QHIWRARRAEPATA 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: 1816
Number of extensions: 71
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 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:

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