GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Escherichia coli BW25113

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 17515 b3454 ATP-binding component of leucine transport (VIMSS)

Query= TCDB::Q55164
         (267 letters)



>FitnessBrowser__Keio:17515
          Length = 237

 Score =  116 bits (291), Expect = 4e-31
 Identities = 79/260 (30%), Positives = 126/260 (48%), Gaps = 34/260 (13%)

Query: 15  ESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGE 74
           E  +L    +S  +G ++A+    + + +G I  LIG NGAGKTTL   L    R   G 
Sbjct: 2   EKVMLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGR 61

Query: 75  VLFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLA------DQHQTGEKFLP 128
           ++F+   I      +I         +  +V SR+TV EN+ +       DQ Q   K++ 
Sbjct: 62  IVFDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWVY 121

Query: 129 RL---INFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNP 185
            L   ++ RR+Q+                         AG +SGG++++L + RALMSNP
Sbjct: 122 ELFPRLHERRIQR-------------------------AGTMSGGEQQMLAIGRALMSNP 156

Query: 186 KLILLDEPAAGVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNL 245
           +L+LLDEP+ G+ P +I QI + I     QG+T  ++E N +  + L    +VL  G  +
Sbjct: 157 RLLLLDEPSLGLAPIIIQQIFDTIEQLREQGMTIFLVEQNANQALKLADRGYVLENGHVV 216

Query: 246 ADGTPEQIQSDPRVLEAYLG 265
              T + + ++  V  AYLG
Sbjct: 217 LSDTGDALLANEAVRSAYLG 236


Lambda     K      H
   0.319    0.136    0.389 

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: 161
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: 267
Length of database: 237
Length adjustment: 24
Effective length of query: 243
Effective length of database: 213
Effective search space:    51759
Effective search space used:    51759
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 (21.7 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