GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natG in Pseudomonas fluorescens FW300-N2E2

Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate Pf6N2E2_5403 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)

Query= TCDB::Q8YPM8
         (308 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5403
          Length = 375

 Score =  153 bits (387), Expect = 5e-42
 Identities = 82/135 (60%), Positives = 99/135 (73%), Gaps = 1/135 (0%)

Query: 175 PEFSALLLGLIFYTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVI 234
           PE  AL L L  YT AFIAEIVR GI+SVS GQ EA RSLGL     +R VI PQALRVI
Sbjct: 241 PELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVI 300

Query: 235 IPPLTSQYLNLTKNSSLAIAIGYPD-IYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTIS 293
           IPPLTSQYLNL KNSSLA  IGYP+ +   A T  NQTG+A+EV+ + M  YL++S++IS
Sbjct: 301 IPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISIS 360

Query: 294 LIMNAFNRTVQIKER 308
           L+MN +N+ + + ER
Sbjct: 361 LLMNWYNKRIALIER 375



 Score =  135 bits (339), Expect = 2e-36
 Identities = 69/175 (39%), Positives = 101/175 (57%), Gaps = 6/175 (3%)

Query: 24  LFLAAFVVAI------LLGNLNRNLQRLGIQFGFDFLKQQASFDIGETLIAYKPTDTYSL 77
           +F    VVA+      L  N   NLQ  GI  GF FL++ A F I + LI Y   D+Y+ 
Sbjct: 5   VFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEADSYAR 64

Query: 78  ALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLF 137
              +GL+N+L + F+G+IL TI+G + G+ARLS NW++  ++ VYVE+FRN P LLQ+LF
Sbjct: 65  VFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQILF 124

Query: 138 WYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFI 192
           WYFAVFL +P      + G    +S  GL +P    +  F   ++ ++    A +
Sbjct: 125 WYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWPFVISVVLAIVAIV 179


Lambda     K      H
   0.328    0.143    0.430 

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: 334
Number of extensions: 19
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 308
Length of database: 375
Length adjustment: 28
Effective length of query: 280
Effective length of database: 347
Effective search space:    97160
Effective search space used:    97160
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: 49 (23.5 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