GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Pseudomonas fluorescens FW300-N1B4

Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate Pf1N1B4_1079 Lipopolysaccharide ABC transporter, ATP-binding protein LptB

Query= CharProtDB::CH_003736
         (237 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1079
          Length = 241

 Score =  127 bits (319), Expect = 2e-34
 Identities = 72/234 (30%), Positives = 127/234 (54%), Gaps = 4/234 (1%)

Query: 6   LSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVFD 65
           L    ++  Y   Q + +VSL I+ G+IV L+G NGAGKTT    + G  +A  GR++ D
Sbjct: 4   LKAQHLAKSYKSRQVVRDVSLSIDSGQIVGLLGPNGAGKTTCFYMIVGLVQADQGRVLID 63

Query: 66  DKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENL-AMGGFFAERDQFQER--IKWVYE 122
           D D++        +  +  +P+   +F +++V +N+ A+     E DQ   R  ++ + +
Sbjct: 64  DLDVSHQPMHGRAKAGIGYLPQEASIFRKLSVADNIMAILETRKELDQAGRRQELESLLQ 123

Query: 123 LFPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQ 182
            F  +H  R     ++SGGE++ + I RAL +NP+ +LLDEP  G+ PI +  I   I  
Sbjct: 124 EF-HIHHIRDNLGMSLSGGERRRVEIARALATNPKFILLDEPFAGVDPISVGDIKQIIHH 182

Query: 183 LREQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLG 236
           L+ +G+ + + + N  + L + +  Y++ +G ++       +LANE V+  YLG
Sbjct: 183 LKAKGIGVLITDHNVRETLDICETAYIVNDGQLIAEGDSATILANELVKEVYLG 236


Lambda     K      H
   0.321    0.137    0.390 

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: 106
Number of extensions: 5
Number of successful extensions: 2
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: 237
Length of database: 241
Length adjustment: 23
Effective length of query: 214
Effective length of database: 218
Effective search space:    46652
Effective search space used:    46652
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: 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