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 1937256 b4485 predicted sugar transporter subunit: ATP-binding component of ABC superfamily (NCBI)

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Keio:1937256
          Length = 500

 Score =  345 bits (884), Expect = 3e-99
 Identities = 201/496 (40%), Positives = 291/496 (58%), Gaps = 20/496 (4%)

Query: 7   TSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTAD 66
           T     +L    + K FPGV+AL  V+ +   GE+ AL+GENGAGKSTL+K L+G Y AD
Sbjct: 3   TDQHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHAD 62

Query: 67  PGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGD 126
            G    ++GQ +       A+ LG+  +YQE++L PN+SVA+N+++GR  +R GL+ R +
Sbjct: 63  RG-TIWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKE 121

Query: 127 MVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHET 186
           M +     +A  G        +   S+A +Q+V I RA+   A++L++DEPT  L T E 
Sbjct: 122 MEKRATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEV 181

Query: 187 DRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMM 246
           + LF L+RQLR  G+++++++H + ++ +++DR+TVLR+G FVG  +   L Q  LVKMM
Sbjct: 182 ELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMM 241

Query: 247 VGRDLSGFYTKTHGQAVEREVMLSVRDVAD----GRRVKGCSFDL--RAGEVLGLAGLVG 300
           +GR+L      TH        +LS + VA     G++     FDL  R GE++GLAGL+G
Sbjct: 242 LGRELD-----THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLG 296

Query: 301 AGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGL 360
           +GRTE A ++FG      G   I     +          P QA   GI +  EDRK  G+
Sbjct: 297 SGRTETAEVIFGIKPADSGTALIKGKPQN-------LRSPHQASVLGIGFCPEDRKTDGI 349

Query: 361 FLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQ 420
               SV ENI L + A+    L  ++R   +      I  LGIR    +  +  LSGGNQ
Sbjct: 350 IAAASVRENIILALQAQRG-WLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQ 408

Query: 421 QKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGL 480
           QKV+LSR L  +P+ LILDEPTRG+D+GA +EI RLI  L   G+A+L+ISSEL E+VG 
Sbjct: 409 QKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGY 468

Query: 481 CDRVLVMREGTLAGEV 496
            DRV++MR+     E+
Sbjct: 469 ADRVIIMRDRKQVAEI 484



 Score = 70.1 bits (170), Expect = 2e-16
 Identities = 64/238 (26%), Positives = 106/238 (44%), Gaps = 11/238 (4%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           P+ A +N  K       +   +L    GE+  L G  G+G++   +++ G   AD  G  
Sbjct: 263 PVAAFKNYGKK----GTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPAD-SGTA 317

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELS---LAPNLSVAENIYLGRALQRRGL--VARGD 126
            I G+   +  P  A  LG+    ++     +    SV ENI L    QR  L  ++R +
Sbjct: 318 LIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKE 377

Query: 127 MVRACAPTLARLGADF-SPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHE 185
                   + +LG    S    +  LS   +Q V ++R +    + L++DEPT  +    
Sbjct: 378 QQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGA 437

Query: 186 TDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALV 243
              +  LI  L  +G+A+L IS  + E+   ADRV ++RD   V  +  A LS  A++
Sbjct: 438 HAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIM 495


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: 577
Number of extensions: 24
Number of successful extensions: 7
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: 500
Length adjustment: 35
Effective length of query: 505
Effective length of database: 465
Effective search space:   234825
Effective search space used:   234825
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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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:

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:

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:

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:

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