GapMind for catabolism of small carbon sources

 

Alignments for a candidate for snatA in Pseudomonas fluorescens FW300-N2E3

Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate AO353_13635 AO353_13635 hypothetical protein

Query= TCDB::Q8J305
         (216 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_13635
          Length = 198

 Score =  114 bits (286), Expect = 1e-30
 Identities = 69/205 (33%), Positives = 113/205 (55%), Gaps = 12/205 (5%)

Query: 8   LKYLILLYGGLFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQW 67
           L  L  +Y  +  + +P   +  F+S+T   S +E+R +A   A++ + + V+  L G+ 
Sbjct: 2   LHVLFSVYLKMLVLYSPFFVLSCFISLTRGYSRKEQRRLAWNVALATLVSSVLLYLFGRV 61

Query: 68  IFKFFGSSTDAFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLEEVAIIPL 127
           IF  FG + DAF I  G +LF  AL M  GK S+V+  N +           ++V I+PL
Sbjct: 62  IFSVFGITVDAFRIGAGSVLFISALGMAQGK-SAVQTDNVQ-----------QDVTIVPL 109

Query: 128 AIPLISGPGAITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKARLGRVGI 187
            IPL  GPG I  +++          +L  IL+I +  +TV  VL  +NRI+  LG  G+
Sbjct: 110 TIPLTVGPGTIGALLVMGVSQPHWDDKLTAILSIAMASLTVGVVLYLSNRIERILGDQGL 169

Query: 188 KVMTRMMGLILTSMAVQMIINGIKG 212
           ++++R+MGL + ++A Q+I  G+KG
Sbjct: 170 QIVSRLMGLFVCALAAQIIFTGVKG 194


Lambda     K      H
   0.327    0.141    0.396 

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: 105
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: 216
Length of database: 198
Length adjustment: 21
Effective length of query: 195
Effective length of database: 177
Effective search space:    34515
Effective search space used:    34515
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 (21.7 bits)
S2: 45 (21.9 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