GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livF 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)



>lcl|FitnessBrowser__Keio:17516 b3455 leucine/isoleucine/valine
           transporter subunit (NCBI)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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