Alignments for a candidate for frcA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Pseudomonas fluorescens GW456-L13

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate PfGW456L13_7 ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_7
          Length = 521

 Score =  256 bits (653), Expect = 2e-72
 Identities = 176/490 (35%), Positives = 251/490 (51%), Gaps = 20/490 (4%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           P L LR I K +PG  A   ++LT   GE+HAL+GENGAGKSTLMKI+ G   AD  GE 
Sbjct: 12  PRLQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHAD-SGEV 70

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
              GQRV +  P  AR LG+ +++Q  SL   LSVA+NI L               +R  
Sbjct: 71  IWQGQRVSLRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAGTPKQLEPKIREV 130

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
           +    R G    P   V SLSI +RQ VEI R +  + R+L++DEPT+ L+  E D LF 
Sbjct: 131 S---RRYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFV 187

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR-- 249
            +R+L  EG +IL+ISH++ E+  L    TVLR G   G    A  S   L ++MVG   
Sbjct: 188 TLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLARLMVGEAA 247

Query: 250 DLSGFYTKTHGQAVEREVMLSVRDVA------DGRRVKGCSFDLRAGEVLGLAGLVGAGR 303
           +L   Y K  G     +  L VR ++       G  +     ++R GE++G+AG+ G G+
Sbjct: 248 ELIADYPKVTG----GDACLDVRGLSWHNPDPFGCSLANIDLEVRRGEIVGIAGVAGNGQ 303

Query: 304 TELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLD 363
            EL  L+ G +A            G   +  L     RQ    G+A++  +R   G   +
Sbjct: 304 DELLALLSG-EALLPRNASATIRFGKEPVAHLRPDARRQ---LGLAFVPAERLGHGAVPE 359

Query: 364 QSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKV 423
            S+ +N  L       +  G + R        E I   G++   +Q    +LSGGN QK 
Sbjct: 360 LSLADNALLTAFQHGLVSNGLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKF 419

Query: 424 MLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDR 483
           +L R +  QPR+L+   PT GVD+GA + I+R + AL  +G AIL+IS +L E+  + DR
Sbjct: 420 ILGREILQQPRLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDR 479

Query: 484 VLVMREGTLA 493
           +  +  G L+
Sbjct: 480 LGALCGGRLS 489



 Score = 74.3 bits (181), Expect = 1e-17
 Identities = 78/263 (29%), Positives = 116/263 (44%), Gaps = 28/263 (10%)

Query: 278 RRVKGC------SFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGG 331
           +R  GC         +  GE+  L G  GAG++ L ++++G      GEV        G 
Sbjct: 21  KRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEV-----IWQGQ 75

Query: 332 LVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAAR 391
            V+L    P QA   GI  + +   L   F   SV +NI L      A+G          
Sbjct: 76  RVSLR--NPAQARGLGIGMVFQHFSL---FETLSVAQNIAL------AMGAAAGTPKQLE 124

Query: 392 RRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKS 451
            +  E     G+ +   ++ V +LS G +Q+V + R L    R+LILDEPT  +      
Sbjct: 125 PKIREVSRRYGMTLEPERL-VHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEAD 183

Query: 452 EIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIA 511
           +++  +  LA  G +IL IS +L EV  LC    V+R G +AG   PA     + +++  
Sbjct: 184 DLFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAEC---SDQQLAR 240

Query: 512 LATGAAAAAPAWVDVPLPGAGNA 534
           L  G AA   A  D P    G+A
Sbjct: 241 LMVGEAAELIA--DYPKVTGGDA 261


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: 657
Number of extensions: 34
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 540
Length of database: 521
Length adjustment: 35
Effective length of query: 505
Effective length of database: 486
Effective search space:   245430
Effective search space used:   245430
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)
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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