GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagB in Shewanella amazonensis SB2B

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate 6936758 Sama_0945 glutamine--fructose-6-phosphate transaminase (isomerizing) (RefSeq)

Query= reanno::SB2B:6936758
         (332 letters)



>lcl|FitnessBrowser__SB2B:6936758 Sama_0945
           glutamine--fructose-6-phosphate transaminase
           (isomerizing) (RefSeq)
          Length = 332

 Score =  631 bits (1628), Expect = 0.0
 Identities = 332/332 (100%), Positives = 332/332 (100%)

Query: 1   MTNTIMEQEARTAPAKIAAQLAANAQITAELGAKLRELNPRFVMIVGRGSSDHAGVFGKY 60
           MTNTIMEQEARTAPAKIAAQLAANAQITAELGAKLRELNPRFVMIVGRGSSDHAGVFGKY
Sbjct: 1   MTNTIMEQEARTAPAKIAAQLAANAQITAELGAKLRELNPRFVMIVGRGSSDHAGVFGKY 60

Query: 61  LFEIETGVPTFAAAPSVASVYGKSLKLEGALVIVISQSGRSPDILAQARMAKNAGAFCVA 120
           LFEIETGVPTFAAAPSVASVYGKSLKLEGALVIVISQSGRSPDILAQARMAKNAGAFCVA
Sbjct: 61  LFEIETGVPTFAAAPSVASVYGKSLKLEGALVIVISQSGRSPDILAQARMAKNAGAFCVA 120

Query: 121 LVNDESAPIKDIVDVVLPLRAGEEKAVAATKSYLCTLSALIQLAAAWTQSESLAKAVDTM 180
           LVNDESAPIKDIVDVVLPLRAGEEKAVAATKSYLCTLSALIQLAAAWTQSESLAKAVDTM
Sbjct: 121 LVNDESAPIKDIVDVVLPLRAGEEKAVAATKSYLCTLSALIQLAAAWTQSESLAKAVDTM 180

Query: 181 PTALEAAVNAEPQLTAEGIGAVRNLVVLGRGLGYAVSKEIALKLKEVCSIHAEAFSSAEF 240
           PTALEAAVNAEPQLTAEGIGAVRNLVVLGRGLGYAVSKEIALKLKEVCSIHAEAFSSAEF
Sbjct: 181 PTALEAAVNAEPQLTAEGIGAVRNLVVLGRGLGYAVSKEIALKLKEVCSIHAEAFSSAEF 240

Query: 241 LHGPVTLVEKKLTIVDVCVGDESYASHIEQIENVSSRGADLVHLNQTSTDIHPRVAPLAL 300
           LHGPVTLVEKKLTIVDVCVGDESYASHIEQIENVSSRGADLVHLNQTSTDIHPRVAPLAL
Sbjct: 241 LHGPVTLVEKKLTIVDVCVGDESYASHIEQIENVSSRGADLVHLNQTSTDIHPRVAPLAL 300

Query: 301 LQRFYIDVAAVAVARGIDPDAPAGLKKVTQTL 332
           LQRFYIDVAAVAVARGIDPDAPAGLKKVTQTL
Sbjct: 301 LQRFYIDVAAVAVARGIDPDAPAGLKKVTQTL 332


Lambda     K      H
   0.316    0.130    0.356 

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: 498
Number of extensions: 8
Number of successful extensions: 1
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: 332
Length of database: 332
Length adjustment: 28
Effective length of query: 304
Effective length of database: 304
Effective search space:    92416
Effective search space used:    92416
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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 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, 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