Alignments for a candidate for Psest_0084 in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Pseudomonas putida KT2440

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate PP_3955 PP_3955 permease

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



>FitnessBrowser__Putida:PP_3955
          Length = 675

 Score = 1042 bits (2694), Expect = 0.0
 Identities = 516/666 (77%), Positives = 592/666 (88%)

Query: 4   SQGLHASPSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYPARG 63
           +QGLHAS   WP ALF VAL+FS++QI TAAF  +S+QVLRA HVGFLLL+V+L Y   G
Sbjct: 5   AQGLHASTDRWPAALFAVALVFSVFQIATAAFPLISTQVLRAIHVGFLLLVVYLSYSFVG 64

Query: 64  NGKPFQPVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARRVM 123
           + +P+QP+AWLLGLAG AT  YQWYFE DLIQRSG++TT+D++VGL LI LVFEAARRVM
Sbjct: 65  HRRPWQPLAWLLGLAGMATAAYQWYFEGDLIQRSGELTTSDLIVGLLLIGLVFEAARRVM 124

Query: 124 GIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYIFL 183
           GIALPIICALFLAYGLLG++LPG+LAHRGY LDQIVNQL+FGTEGLYGTPTYVSATYI+L
Sbjct: 125 GIALPIICALFLAYGLLGQHLPGELAHRGYGLDQIVNQLAFGTEGLYGTPTYVSATYIYL 184

Query: 184 FILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTGQF 243
           FILFG+FLEQAGMI+LFTDFAMGLFGH+ GGPAKVSV SSALMGTITGSGVANVVTTGQF
Sbjct: 185 FILFGAFLEQAGMIRLFTDFAMGLFGHRSGGPAKVSVFSSALMGTITGSGVANVVTTGQF 244

Query: 244 TIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPAL 303
           TIPLMKRFGY+PAFAGGVEATSSMGSQ+MPPVMGAVAFIMAETINVP+ E+AKAALIPAL
Sbjct: 245 TIPLMKRFGYKPAFAGGVEATSSMGSQLMPPVMGAVAFIMAETINVPYAEVAKAALIPAL 304

Query: 304 LYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTPMFA 363
           LYFGSV+WMVHLEA+R+ L GLP+++CPSA  A+++RW+LL+PL+VLV LLFSGRTP+++
Sbjct: 305 LYFGSVYWMVHLEARRSHLHGLPREQCPSAWDALRQRWFLLVPLMVLVALLFSGRTPLYS 364

Query: 364 GTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALVAVC 423
           G +GLALTAIVILGSAIIL+     LR AFW+ALG+LC+GFF++GIGVI  VIA L   C
Sbjct: 365 GMVGLALTAIVILGSAIILRAQKTWLRAAFWVALGILCSGFFRMGIGVILMVIAGLAIAC 424

Query: 424 WFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAVGEN 483
            F++GGR TL  C+ AL EGARHAVPVGIACALVGVIIGV+SLTG+A+TFAGYIL +G +
Sbjct: 425 CFVQGGRATLHACVMALAEGARHAVPVGIACALVGVIIGVISLTGLATTFAGYILDLGRD 484

Query: 484 NLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIMADL 543
           NLFLSL+LTMLTCLVLGMGIPTIPNYIITSSIAAPALL+LGVPLIVSHMFVFYFGI+ADL
Sbjct: 485 NLFLSLVLTMLTCLVLGMGIPTIPNYIITSSIAAPALLELGVPLIVSHMFVFYFGILADL 544

Query: 544 TPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATLYML 603
           TPPVALACFAAAPIAKE+GL IS WA+RIA+AGF+VPFMAVY+PALMMQG   G+TLYM+
Sbjct: 545 TPPVALACFAAAPIAKEKGLLISFWAVRIALAGFVVPFMAVYDPALMMQGDSMGSTLYMV 604

Query: 604 FKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFLIQHI 663
            KAAFAV LWG    G+L+ PM  WE++LAFAA  S++LA PISDE+GFALGA  L  H 
Sbjct: 605 IKAAFAVALWGCASIGHLRAPMPWWERLLAFAAGVSLILAAPISDEVGFALGAAVLGWHY 664

Query: 664 WRARRA 669
           WR R A
Sbjct: 665 WRTRPA 670


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: 1637
Number of extensions: 86
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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