GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Fibrella aestuarina BUZ 2

Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate WP_015334118.1 FAES_RS25660 ABC transporter ATP-binding protein

Query= TCDB::P0A9S7
         (255 letters)



>NCBI__GCF_000331105.1:WP_015334118.1
          Length = 221

 Score =  113 bits (282), Expect = 4e-30
 Identities = 68/230 (29%), Positives = 118/230 (51%), Gaps = 19/230 (8%)

Query: 4   PLLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTIL 63
           P+L    L   +G L  +N+V+L +   E+VS++G +GAGK+T+ + L    +P GG++ 
Sbjct: 2   PILHATNLRRAYGPLPVLNDVSLSIDAGEVVSIVGASGAGKSTLLHILGTLDRPDGGSVT 61

Query: 64  LRDQHLEGLPGQQIARMG---VVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKT 120
           L  Q +  L  +Q+AR     +   FQ   L  E T +EN+ +        G   G    
Sbjct: 62  LAGQDVFSLTDKQLARFRNEQIGFVFQFHNLLPEFTALENVAIP-------GFIGG---- 110

Query: 121 PSFRRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEP 180
               R +     RAA  L R+GL +      + L+ G+Q+R+ +AR ++ QP ++  DEP
Sbjct: 111 ----RDEKAVRQRAAELLSRLGLADRQQHFPAQLSGGEQQRVAVARALINQPAVVFADEP 166

Query: 181 AAGLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQG 230
           +  L+ +  +EL +L  +LR+    T +++ H+  L M ++DR   +  G
Sbjct: 167 SGNLDSRNAEELHQLFFDLRDTFGQTFIIVTHNETLAM-LADRSITLRDG 215


Lambda     K      H
   0.320    0.137    0.395 

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: 139
Number of extensions: 8
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: 255
Length of database: 221
Length adjustment: 23
Effective length of query: 232
Effective length of database: 198
Effective search space:    45936
Effective search space used:    45936
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 24 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