GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Pseudomonas fluorescens FW300-N2C3

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate AO356_10240 AO356_10240 amino acid ABC transporter permease

Query= TCDB::Q52665
         (434 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_10240
          Length = 221

 Score = 89.4 bits (220), Expect = 1e-22
 Identities = 71/231 (30%), Positives = 116/231 (50%), Gaps = 18/231 (7%)

Query: 204 IEAALQSALPLALPEVDSDQF--GGFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKS 261
           +EAALQ AL       DS  F   G    +++ +  +   L LG  LAL R S   +V  
Sbjct: 1   MEAALQLAL-------DSAPFLLKGAYYTVILSLGGMFFGLLLGFGLALMRLSRFKLVSW 53

Query: 262 LSVGIIEFVRGVPLITLLFTASLLLQYFLPP-GTNFDLILRVVILVTLFAAAYIAEVIRG 320
           ++   + F RG PL+  LF    ++ Y LP  G   D +   +I  +L  AAY  E++R 
Sbjct: 54  IARIYVSFFRGTPLLVQLF----VIYYGLPQLGIELDPLPAALIGFSLNMAAYACEILRA 109

Query: 321 GLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLF 380
            ++++ RGQ+EAA ++G+   Q  R  I+PQA + ++P + +SFI L KDT L A + + 
Sbjct: 110 AISSIERGQWEAAASIGMTRAQTLRRAILPQAARTALPPLGNSFISLVKDTALAATIQVP 169

Query: 381 DPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMSRYSMYLERKLKR 431
           +  +    +     A     +  Y+  ALI+++    +S     LE ++ R
Sbjct: 170 ELFRQAQLIT----ARTFEIFTMYLAAALIYWVLATVLSHLQNVLEARVNR 216


Lambda     K      H
   0.329    0.143    0.457 

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: 240
Number of extensions: 13
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: 434
Length of database: 221
Length adjustment: 27
Effective length of query: 407
Effective length of database: 194
Effective search space:    78958
Effective search space used:    78958
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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