GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1692 in Escherichia coli BW25113

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 17516 b3455 leucine/isoleucine/valine transporter subunit (NCBI)

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__Keio:17516
          Length = 255

 Score =  125 bits (313), Expect = 1e-33
 Identities = 79/251 (31%), Positives = 134/251 (53%), Gaps = 18/251 (7%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68
           LL V GL + +GG+ AV  V+ E+   E+VSLIG NGAGKTT    +TG      G I  
Sbjct: 5   LLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILL 64

Query: 69  LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILAD------- 121
             + ++G     + + G+V   +   +F  MT+ ENL +  + ++ K G+ +        
Sbjct: 65  RDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQH-QQLKTGLFSGLLKTPSF 123

Query: 122 -------IEKMFTIFPR--LRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMG 172
                  +++  T   R  L E  ++ A  ++ G+Q+ L + R +++QP++L+LDEP+ G
Sbjct: 124 RRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAG 183

Query: 173 LSPIMVDKIFEVVRDV-YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLN 231
           L+P    ++ E++ ++      TI+L+E +    + I+DR YV+  G     G  +Q+ N
Sbjct: 184 LNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIRN 243

Query: 232 DPKVRAAYLGE 242
           +P V  AYLGE
Sbjct: 244 NPDVIRAYLGE 254


Lambda     K      H
   0.317    0.136    0.373 

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: 144
Number of extensions: 8
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 242
Length of database: 255
Length adjustment: 24
Effective length of query: 218
Effective length of database: 231
Effective search space:    50358
Effective search space used:    50358
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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