Alignments for a candidate for Psest_0084 in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Pseudomonas fluorescens FW300-N2E2

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate Pf6N2E2_320 TRAP transporter, 4TM/12TM fusion protein, unknown substrate 1

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_320
          Length = 675

 Score = 1094 bits (2830), Expect = 0.0
 Identities = 542/675 (80%), Positives = 603/675 (89%), Gaps = 1/675 (0%)

Query: 1   MSESQ-GLHASPSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCY 59
           MSE Q G+   P +WP+ LFYVALLFSI+QIVTAAF PVSS VLRA HVGFLL +VFL Y
Sbjct: 1   MSEDQHGIATDPRDWPKTLFYVALLFSIFQIVTAAFSPVSSIVLRAVHVGFLLWVVFLSY 60

Query: 60  PARGNGKPFQPVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAA 119
           PA G  +P+QP+AW+L L G AT  YQW FE+DLIQRSGD+TT DM++G+ L+VLVFEAA
Sbjct: 61  PAHGRQRPWQPLAWVLSLGGVATALYQWVFESDLIQRSGDLTTTDMIMGIVLVVLVFEAA 120

Query: 120 RRVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSAT 179
           RRVMGIALPIIC LFLAYGL GEYLPGDLAHRGY LDQI+NQLSFGTEGLYGTPTYVSAT
Sbjct: 121 RRVMGIALPIICGLFLAYGLFGEYLPGDLAHRGYGLDQIINQLSFGTEGLYGTPTYVSAT 180

Query: 180 YIFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVT 239
           YIFLFILFG+FLE+AGMIKLFTDFAMGLFGHKLGGPAKV+VVSSALMGTITGSG+ANVVT
Sbjct: 181 YIFLFILFGAFLEKAGMIKLFTDFAMGLFGHKLGGPAKVAVVSSALMGTITGSGIANVVT 240

Query: 240 TGQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAAL 299
           TGQFTIPLMKRFGY+ AFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAAL
Sbjct: 241 TGQFTIPLMKRFGYKAAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAAL 300

Query: 300 IPALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRT 359
           IPA LYFGSVFWMVHLEAKR+ LKGLPKD+CPSA  AVK+ W+LLIPL VLV+LLFSGRT
Sbjct: 301 IPACLYFGSVFWMVHLEAKRSDLKGLPKDQCPSAWGAVKDSWFLLIPLGVLVYLLFSGRT 360

Query: 360 PMFAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAAL 419
           P+F+G +GLALTAIVILGSAIILKVSN+ALR AFWIALGLLC GFF+LGIGV+F VI  L
Sbjct: 361 PLFSGMVGLALTAIVILGSAIILKVSNYALRCAFWIALGLLCVGFFRLGIGVVFAVIGVL 420

Query: 420 VAVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILA 479
           V  CWF++G R+TLVICLHALV+GARHAVPVGIACALVG II VVSLTGVASTFAGYILA
Sbjct: 421 VVACWFMQGTRETLVICLHALVDGARHAVPVGIACALVGSIIAVVSLTGVASTFAGYILA 480

Query: 480 VGENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGI 539
           +G +NL LSL+LTMLTCLVLGMGIPTIPNYIITSSIAAPALL+LGVPLIVSHMFVFYFGI
Sbjct: 481 IGRDNLLLSLILTMLTCLVLGMGIPTIPNYIITSSIAAPALLELGVPLIVSHMFVFYFGI 540

Query: 540 MADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGAT 599
           +ADLTPPVALACFAAAPIA+E GLKIS WA+RIA+AGF++PFM VYNPALM+QG +   T
Sbjct: 541 LADLTPPVALACFAAAPIARESGLKISFWAVRIALAGFVIPFMTVYNPALMLQGDNLWMT 600

Query: 600 LYMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFL 659
            YML K   AVGLWG   TGYLQ+ M +WE++L FAA A +V+A+P++DEIGF LG L +
Sbjct: 601 AYMLIKTLLAVGLWGMASTGYLQQKMPIWERLLCFAAGALLVVALPVTDEIGFVLGGLLI 660

Query: 660 IQHIWRARRAEPATA 674
           +QH+WRARR+  A A
Sbjct: 661 LQHVWRARRSGRALA 675


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: 1691
Number of extensions: 83
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: 675
Length adjustment: 39
Effective length of query: 635
Effective length of database: 636
Effective search space:   403860
Effective search space used:   403860
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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