GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Psest_0084 in Pseudomonas litoralis 2SM5

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate WP_090275379.1 BLU11_RS16790 TRAP transporter permease

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



>NCBI__GCF_900105005.1:WP_090275379.1
          Length = 674

 Score = 1178 bits (3048), Expect = 0.0
 Identities = 579/674 (85%), Positives = 627/674 (93%)

Query: 1   MSESQGLHASPSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYP 60
           MSE +GL ASP++WPRALFYVALLFS YQIVTAAFHPVS+QVLRAGHVGFLLLLV+L YP
Sbjct: 1   MSEDRGLSASPADWPRALFYVALLFSCYQIVTAAFHPVSTQVLRAGHVGFLLLLVYLSYP 60

Query: 61  ARGNGKPFQPVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAAR 120
            RGN +P+QP+AW+LGLAG ATF YQWYFEADLIQRSGD+TT DMVVG+ LI LVFEAAR
Sbjct: 61  LRGNARPWQPLAWILGLAGMATFAYQWYFEADLIQRSGDLTTTDMVVGIILIALVFEAAR 120

Query: 121 RVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATY 180
           RVMGIALPIIC LFLAYGL G +LPGDLAHRGYYLDQ+VNQLSFGTEGLYGTPTYVSATY
Sbjct: 121 RVMGIALPIICGLFLAYGLFGNHLPGDLAHRGYYLDQVVNQLSFGTEGLYGTPTYVSATY 180

Query: 181 IFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTT 240
           IFLFILFGSFLEQAGMI+LFTDFAMGLFGHK GGPAKVSVVSSALMGTITGSGVANVVTT
Sbjct: 181 IFLFILFGSFLEQAGMIRLFTDFAMGLFGHKAGGPAKVSVVSSALMGTITGSGVANVVTT 240

Query: 241 GQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALI 300
           GQFTIPLMKRFGYR AFAGGVEATSSMGSQIMPPVMGAVAFIMAETIN+P+VE+AKAAL+
Sbjct: 241 GQFTIPLMKRFGYRSAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINMPYVEVAKAALL 300

Query: 301 PALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTP 360
           PALLYFGSVFWMVHLEA+R+ L GLPKDECPSA AAVK+RW+LLIPL VL+WLLFSGRTP
Sbjct: 301 PALLYFGSVFWMVHLEARRSKLNGLPKDECPSAWAAVKQRWFLLIPLAVLIWLLFSGRTP 360

Query: 361 MFAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALV 420
           MFAGTIGLALTAIVILGSA+IL+VS+ A+R+ FW+ALG+LCAGFFQLGIGVIFGVI  LV
Sbjct: 361 MFAGTIGLALTAIVILGSALILRVSSTAIRLIFWVALGVLCAGFFQLGIGVIFGVIGVLV 420

Query: 421 AVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAV 480
           A CWFIKGGRDTL+ICLHALVEGARHA+PVGIAC LVGVIIG+VSLTGVASTFAGYILA+
Sbjct: 421 AACWFIKGGRDTLLICLHALVEGARHAIPVGIACVLVGVIIGIVSLTGVASTFAGYILAI 480

Query: 481 GENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIM 540
           G++NLFLSLLLTMLTCL+LGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIM
Sbjct: 481 GQDNLFLSLLLTMLTCLMLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIM 540

Query: 541 ADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATL 600
           ADLTPPVALACFAAAPIA+  GLKISMWAIRIA+AGF+VPFMAVYNPALMMQGGDW ATL
Sbjct: 541 ADLTPPVALACFAAAPIARASGLKISMWAIRIAVAGFVVPFMAVYNPALMMQGGDWAATL 600

Query: 601 YMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFLI 660
           YMLFKAAFA+GLWG VFTGY  + +  WE  L F A   M+LA+PISDE+GFALGA+F+ 
Sbjct: 601 YMLFKAAFAIGLWGTVFTGYFMQRLTWWELPLGFVAGGLMILALPISDELGFALGAVFVA 660

Query: 661 QHIWRARRAEPATA 674
           QH WRARRA  A A
Sbjct: 661 QHWWRARRALTAAA 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: 1767
Number of extensions: 84
Number of successful extensions: 3
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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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