GapMind for catabolism of small carbon sources

 

Aligments for a candidate for garK in Escherichia coli BW25113

Align Glycerate 3-kinase; D-Glycerate-3-kinase; Glycerate kinase 2; GK2; EC 2.7.1.31 (characterized)
to candidate 14651 b0514 glycerate kinase II (NCBI)

Query= SwissProt::P77364
         (381 letters)



>lcl|FitnessBrowser__Keio:14651 b0514 glycerate kinase II (NCBI)
          Length = 381

 Score =  745 bits (1923), Expect = 0.0
 Identities = 381/381 (100%), Positives = 381/381 (100%)

Query: 1   MKIVIAPDSFKESLSAEKCCQAIKAGFSTLFPDANYICLPIADGGEGTVDAMVAATGGNI 60
           MKIVIAPDSFKESLSAEKCCQAIKAGFSTLFPDANYICLPIADGGEGTVDAMVAATGGNI
Sbjct: 1   MKIVIAPDSFKESLSAEKCCQAIKAGFSTLFPDANYICLPIADGGEGTVDAMVAATGGNI 60

Query: 61  VTLEVCGPMGEKVNAFYGLTGDGKTAVIEMAAASGLMLVAPEKRNPLLASSFGTGELIRH 120
           VTLEVCGPMGEKVNAFYGLTGDGKTAVIEMAAASGLMLVAPEKRNPLLASSFGTGELIRH
Sbjct: 61  VTLEVCGPMGEKVNAFYGLTGDGKTAVIEMAAASGLMLVAPEKRNPLLASSFGTGELIRH 120

Query: 121 ALDNDIRHIILGIGGSATVDGGMGMAQALGVRFLDADGQALAANGGNLARVASIEMDECD 180
           ALDNDIRHIILGIGGSATVDGGMGMAQALGVRFLDADGQALAANGGNLARVASIEMDECD
Sbjct: 121 ALDNDIRHIILGIGGSATVDGGMGMAQALGVRFLDADGQALAANGGNLARVASIEMDECD 180

Query: 181 PRLANCHIEVACDVDNPLVGARGAAAVFGPQKGATPEMVEELEQGLQNYARVLQQQTEIN 240
           PRLANCHIEVACDVDNPLVGARGAAAVFGPQKGATPEMVEELEQGLQNYARVLQQQTEIN
Sbjct: 181 PRLANCHIEVACDVDNPLVGARGAAAVFGPQKGATPEMVEELEQGLQNYARVLQQQTEIN 240

Query: 241 VCQMAGGGAAGGMGIAAAVFLNADIKPGIEIVLNAVNLAQAVQGAALVITGEGRIDSQTA 300
           VCQMAGGGAAGGMGIAAAVFLNADIKPGIEIVLNAVNLAQAVQGAALVITGEGRIDSQTA
Sbjct: 241 VCQMAGGGAAGGMGIAAAVFLNADIKPGIEIVLNAVNLAQAVQGAALVITGEGRIDSQTA 300

Query: 301 GGKAPLGVASVAKQFNVPVIGIAGVLGDGVEVVHQYGIDAVFSILPRLAPLAEVLASGET 360
           GGKAPLGVASVAKQFNVPVIGIAGVLGDGVEVVHQYGIDAVFSILPRLAPLAEVLASGET
Sbjct: 301 GGKAPLGVASVAKQFNVPVIGIAGVLGDGVEVVHQYGIDAVFSILPRLAPLAEVLASGET 360

Query: 361 NLFNSARNIACAIKIGQGIKN 381
           NLFNSARNIACAIKIGQGIKN
Sbjct: 361 NLFNSARNIACAIKIGQGIKN 381


Lambda     K      H
   0.318    0.136    0.391 

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: 725
Number of extensions: 19
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: 381
Length of database: 381
Length adjustment: 30
Effective length of query: 351
Effective length of database: 351
Effective search space:   123201
Effective search space used:   123201
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: 50 (23.9 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 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