Alignments for a candidate for frcA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Escherichia coli BW25113

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Keio:17809
          Length = 501

 Score =  382 bits (982), Expect = e-110
 Identities = 218/504 (43%), Positives = 311/504 (61%), Gaps = 15/504 (2%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72
           LL L+ I K FPGV+AL    L  Y G V AL+GENGAGKST+MK+L+G YT D G    
Sbjct: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63

Query: 73  IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMVRAC 131
           + G+     GP+S+++ G+ +I+QEL+L P L++AENI+LGR    R G +    M    
Sbjct: 64  L-GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEA 122

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
              LA+L   F     V  LSI  +Q+VEIA+ + FE+++++MDEPT  L+  ET+ LF 
Sbjct: 123 DKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFR 182

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251
           +IR+L+ +G  I+YISHRM EI E+ D VTV RDG F+   + A L++ +L++MMVGR L
Sbjct: 183 VIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKL 242

Query: 252 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 311
              Y   H      ++ L V ++  G  V   SF LR GE+LG++GL+GAGRTEL ++++
Sbjct: 243 EDQYP--HLDKAPGDIRLKVDNLC-GPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLY 299

Query: 312 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 371
           GA  RT G V +           +    P+  +  GI Y++EDRK  GL L  SV EN++
Sbjct: 300 GALPRTSGYVTLDGHE-------VVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMS 352

Query: 372 LIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431
           L      +   G L     ++  ++ I    ++    +  +G LSGGNQQKV ++R L  
Sbjct: 353 LTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMT 412

Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491
           +P+VLILDEPTRGVD+GAK EIY+LIN     G++I+++SSE+PEV+G+ DR++VM EG 
Sbjct: 413 RPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGH 472

Query: 492 LAGEVRPAGSAAETQERIIALATG 515
           L+GE         TQE ++A A G
Sbjct: 473 LSGEFT---REQATQEVLMAAAVG 493



 Score = 88.6 bits (218), Expect = 5e-22
 Identities = 70/243 (28%), Positives = 112/243 (46%), Gaps = 13/243 (5%)

Query: 14  LALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHI 73
           L + N+C   PGV     V  T   GE+  + G  GAG++ LMK+L GA      G   +
Sbjct: 258 LKVDNLCG--PGVN---DVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRT-SGYVTL 311

Query: 74  DGQRVQIDGPQSARDLGVAVIYQELS---LAPNLSVAENIYLG--RALQRRGLVARGDMV 128
           DG  V    PQ     G+  I ++     L   +SV EN+ L   R   R G   +    
Sbjct: 312 DGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADE 371

Query: 129 RACAPTLARLGADFSPAAN--VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHET 186
           +       RL    +P+    +  LS   +Q V IAR +    ++L++DEPT  +     
Sbjct: 372 QQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAK 431

Query: 187 DRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMM 246
             ++ LI Q + +G++I+ +S  M E+  ++DR+ V+ +G   G   R   +Q  L+   
Sbjct: 432 KEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAA 491

Query: 247 VGR 249
           VG+
Sbjct: 492 VGK 494


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: 591
Number of extensions: 31
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: 501
Length adjustment: 35
Effective length of query: 505
Effective length of database: 466
Effective search space:   235330
Effective search space used:   235330
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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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