GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natG in Pseudomonas fluorescens FW300-N2E3

Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate AO353_04610 AO353_04610 amino acid ABC transporter permease

Query= TCDB::Q8YPM8
         (308 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_04610 AO353_04610 amino acid
           ABC transporter permease
          Length = 393

 Score =  153 bits (386), Expect = 7e-42
 Identities = 82/135 (60%), Positives = 98/135 (72%), Gaps = 1/135 (0%)

Query: 175 PEFSALLLGLIFYTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVI 234
           PE  AL L L  YT AFIAEIVR GI SVS GQ EA RSLGL     +R VI PQALRVI
Sbjct: 259 PELLALTLALTVYTAAFIAEIVRSGINSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVI 318

Query: 235 IPPLTSQYLNLTKNSSLAIAIGYPD-IYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTIS 293
           IPPLTSQYLNL KNSSLA  IGYP+ +   A T  NQTG+A+EV+ + M  YL++S++IS
Sbjct: 319 IPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISIS 378

Query: 294 LIMNAFNRTVQIKER 308
           L+MN +N+ + + ER
Sbjct: 379 LLMNWYNKRIALIER 393



 Score =  137 bits (345), Expect = 4e-37
 Identities = 67/166 (40%), Positives = 99/166 (59%)

Query: 20  QLIALFLAAFVVAILLGNLNRNLQRLGIQFGFDFLKQQASFDIGETLIAYKPTDTYSLAL 79
           Q+I +     +   L  N   NLQ  GI  GF FL++ A F I + LI Y  +D+Y+   
Sbjct: 25  QIITIVAVISMGWYLFNNTQTNLQHRGITSGFSFLERSAGFGIAQHLIDYTESDSYARVF 84

Query: 80  WVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLFWY 139
            +GL+N+L + F+G+IL TI+G + G+ARLS NW++  ++ VYVE FRN P LLQ+LFWY
Sbjct: 85  VIGLLNTLLVTFIGVILATILGFIVGVARLSKNWIINKLATVYVETFRNIPPLLQILFWY 144

Query: 140 FAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLI 185
           FAVFL +P   N  +      +S  GL +P    +  F A ++ ++
Sbjct: 145 FAVFLTMPGPRNSHNFADTFFVSSRGLNMPAAQMANGFWAFVISIV 190


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: 355
Number of extensions: 22
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: 393
Length adjustment: 29
Effective length of query: 279
Effective length of database: 364
Effective search space:   101556
Effective search space used:   101556
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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