Alignments for a candidate for HSERO_RS03640 in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Escherichia coli BW25113

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__Keio:16258
          Length = 506

 Score =  375 bits (962), Expect = e-108
 Identities = 196/494 (39%), Positives = 303/494 (61%), Gaps = 4/494 (0%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           LL+M GI KSF    AL +++L +RP  IHALMGENGAGKSTL+K L G++  D G IL 
Sbjct: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72

Query: 66  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125
            G+ +       +   GI++++QEL +    SV  N+++G    T+   +D   M   T 
Sbjct: 73  QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLG-RYPTKGMFVDQDKMYRETK 131

Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
           A+  +L          G LS+++ Q +EIA+A  + ++IVIMDEPT++L+E+E   LF +
Sbjct: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245
           +R+L++ G  I+YISH+M E++ L D VTVLRDG ++       +  ++I+ MMVGRSL+
Sbjct: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251

Query: 246 EFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARLL 305
           + +  +   P +   +  V  + +L    IR  SFD+  GE+LG AGLVGA RT++   L
Sbjct: 252 QRFPDKENKPGEV--ILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309

Query: 306 FGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM-NVAS 364
           FG   +S G I L G+ ++      A+  G A V E+R+  G++  + +  N+ + N+ +
Sbjct: 310 FGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369

Query: 365 RHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLI 424
              ++GL+ +  +    +  I  + VK     T +G LSGGNQQKV++ RWL   P++L+
Sbjct: 370 YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429

Query: 425 LDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELA 484
           LDEPTRG+D+ AK EIYQL+  LA +G  +++ISSE+PE++GI DR+LVM  G+++G + 
Sbjct: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489

Query: 485 GAAITQENIMRLAT 498
               TQ  I+RLA+
Sbjct: 490 TKTTTQNEILRLAS 503



 Score = 88.6 bits (218), Expect = 5e-22
 Identities = 61/241 (25%), Positives = 112/241 (46%), Gaps = 15/241 (6%)

Query: 274 KIRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMR 333
           K+RP S     GE        GAG++ L + LFG   +  G IL +G+ +     + A+ 
Sbjct: 35  KVRPHSIHALMGEN-------GAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHSAKEALE 87

Query: 334 AGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGL-VRSRSLGGVARAAIQRLNVKV 392
            GI+ V ++     L LQ +V  N  +    R+   G+ V    +    +A    L++ +
Sbjct: 88  NGISMVHQELN---LVLQRSVMDNMWLG---RYPTKGMFVDQDKMYRETKAIFDELDIDI 141

Query: 393 AHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGV 452
             P   VG LS    Q + +A+      K++I+DEPT  +     + ++ ++ +L  +G 
Sbjct: 142 -DPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGC 200

Query: 453 AVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPASHSS 512
            +V IS ++ E+  +CD V V+R+G        A +T + I+ +    ++ +  P   + 
Sbjct: 201 GIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLNQRFPDKENK 260

Query: 513 P 513
           P
Sbjct: 261 P 261


Lambda     K      H
   0.320    0.135    0.378 

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: 589
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: 521
Length of database: 506
Length adjustment: 35
Effective length of query: 486
Effective length of database: 471
Effective search space:   228906
Effective search space used:   228906
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:

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