GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Escherichia coli BW25113

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 1937256 b4485 predicted sugar transporter subunit: ATP-binding component of ABC superfamily (NCBI)

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__Keio:1937256
          Length = 500

 Score =  158 bits (400), Expect = 2e-43
 Identities = 88/224 (39%), Positives = 138/224 (61%), Gaps = 9/224 (4%)

Query: 4   EPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEI 63
           + IL   GL K +  V ALD  DF L  GEI+A++G+NGAGKS++IKA++G    D G I
Sbjct: 7   QEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTI 66

Query: 64  RLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDR 123
            LEG+ I  ++   A+Q GI TVYQ + L P +S+ADN+F+GRE ++ G+       L R
Sbjct: 67  WLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGL-------LRR 119

Query: 124 AAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALG 183
             MEK+A   ++  G     ++ + +   S   +Q VA+ RA    +KV+I+DEPTA+L 
Sbjct: 120 KEMEKRATELMASYGFSL--DVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLD 177

Query: 184 VKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLG 227
            +E   + +L+  +R RG+ ++ ++H +  V++V+DRI + R G
Sbjct: 178 TQEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNG 221



 Score = 92.4 bits (228), Expect = 2e-23
 Identities = 61/215 (28%), Positives = 107/215 (49%), Gaps = 9/215 (4%)

Query: 14  KRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFR 73
           K YG+   +   D ++ PGEI+ + G  G+G++   + I G    D G   ++GKP   R
Sbjct: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327

Query: 74  SPMEARQAGIETVYQNL---ALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQA 130
           SP +A   GI    ++     +  A S+ +N+ L  + ++      W R + R   ++ A
Sbjct: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR-----GWLRPISRKEQQEIA 382

Query: 131 RAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRV 190
              + +LG+ T  +  Q +E LSGG +Q V ++R      + +I+DEPT  + V     +
Sbjct: 383 ERFIRQLGIRT-PSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEI 441

Query: 191 LELILDVRRRGLPIVLISHNMPHVFEVADRIHIHR 225
           + LI  +   GL +++IS  +  +   ADR+ I R
Sbjct: 442 IRLIETLCADGLALLVISSELEELVGYADRVIIMR 476


Lambda     K      H
   0.321    0.136    0.383 

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: 296
Number of extensions: 13
Number of successful extensions: 4
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: 260
Length of database: 500
Length adjustment: 29
Effective length of query: 231
Effective length of database: 471
Effective search space:   108801
Effective search space used:   108801
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: 49 (23.5 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