Alignments for a candidate for frcA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Pseudomonas putida KT2440

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Putida:PP_2759
          Length = 512

 Score =  328 bits (842), Expect = 2e-94
 Identities = 203/509 (39%), Positives = 287/509 (56%), Gaps = 15/509 (2%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           P+L LR I KTF   RAL    L   AG VH L+GENGAGKSTL+K+L+G +  D  G  
Sbjct: 4   PVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPD-AGSL 62

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
            +DGQ      P+    LG+  I+QE  L    +V E ++ G   +   L+ R    R  
Sbjct: 63  LLDGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQREA 122

Query: 132 APTLAR-LGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190
           A  L    G      A +  LS A++Q+V+I RA+  + R+LV DEP+  L   E +RL 
Sbjct: 123 ARLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLL 182

Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250
            ++++LR +G+AI+YISH + EI+ L DRVTVLR+G  V  +   + S   + ++MV R+
Sbjct: 183 RIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNRE 242

Query: 251 LSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLV 310
           +   Y K    A    ++L VR +   R  +G    +R GE++GL GLVG+G  EL R +
Sbjct: 243 VGELYPKVAVPA--GALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSL 300

Query: 311 FGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENI 370
           FG      GEVR+           L    PR+A+  G+A + E+R+ QG+ LD SV EN 
Sbjct: 301 FGLAPPDSGEVRLDGQP-------LSLRSPREAVAQGVALMPEERRRQGVALDLSVQENT 353

Query: 371 NLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLE 430
            L   +R  + LG L+    R  T E I+ L I+   A   V  LSGGNQQKV L++   
Sbjct: 354 TLAALSR-FVRLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFA 412

Query: 431 IQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREG 490
               + +LDEP+ G+D+GAK EIYRLI  L + G  +L++SS+LPE++GLCDR+ VM  G
Sbjct: 413 RCSSLYLLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRG 472

Query: 491 TLAGEVRPAGSAAETQERIIALATGAAAA 519
            +A     AG A    +R++A+ATGA  A
Sbjct: 473 AIAARF-AAGEA--NSDRLLAVATGAQRA 498


Lambda     K      H
   0.320    0.136    0.382 

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: 664
Number of extensions: 38
Number of successful extensions: 9
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: 540
Length of database: 512
Length adjustment: 35
Effective length of query: 505
Effective length of database: 477
Effective search space:   240885
Effective search space used:   240885
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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)
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