GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagK in Shewanella amazonensis SB2B

Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate 6936757 Sama_0944 hypothetical protein (RefSeq)

Query= reanno::SB2B:6936757
         (301 letters)



>lcl|FitnessBrowser__SB2B:6936757 Sama_0944 hypothetical protein
           (RefSeq)
          Length = 301

 Score =  593 bits (1529), Expect = e-174
 Identities = 301/301 (100%), Positives = 301/301 (100%)

Query: 1   MAFDQTLEGQLYLGIDGGGSKCRATLYNNKLDVLGTGVAGRANPLFGLEQTFESILASTE 60
           MAFDQTLEGQLYLGIDGGGSKCRATLYNNKLDVLGTGVAGRANPLFGLEQTFESILASTE
Sbjct: 1   MAFDQTLEGQLYLGIDGGGSKCRATLYNNKLDVLGTGVAGRANPLFGLEQTFESILASTE 60

Query: 61  MALRDAGLSLNDASLLVAGLGLAGVNVPRLLADVQAWQHPFKTMYVTSDLHTACIGAHQG 120
           MALRDAGLSLNDASLLVAGLGLAGVNVPRLLADVQAWQHPFKTMYVTSDLHTACIGAHQG
Sbjct: 61  MALRDAGLSLNDASLLVAGLGLAGVNVPRLLADVQAWQHPFKTMYVTSDLHTACIGAHQG 120

Query: 121 GDGAVIITGTGSCGYVHVGDESLSLGGHGFALGDKGSGAWLGLRAAEHVLLQLDGFAEPT 180
           GDGAVIITGTGSCGYVHVGDESLSLGGHGFALGDKGSGAWLGLRAAEHVLLQLDGFAEPT
Sbjct: 121 GDGAVIITGTGSCGYVHVGDESLSLGGHGFALGDKGSGAWLGLRAAEHVLLQLDGFAEPT 180

Query: 181 ALTERLFANLGVSDALGIVENLAGRSSSCYATLAREVFAAADEGDKVAVGILREGAAYIS 240
           ALTERLFANLGVSDALGIVENLAGRSSSCYATLAREVFAAADEGDKVAVGILREGAAYIS
Sbjct: 181 ALTERLFANLGVSDALGIVENLAGRSSSCYATLAREVFAAADEGDKVAVGILREGAAYIS 240

Query: 241 EMARKLFTLEPARFSMIGGLAEPLQKWLDADVVARLEPSLAAPETGAVLFAIQQHNKQSA 300
           EMARKLFTLEPARFSMIGGLAEPLQKWLDADVVARLEPSLAAPETGAVLFAIQQHNKQSA
Sbjct: 241 EMARKLFTLEPARFSMIGGLAEPLQKWLDADVVARLEPSLAAPETGAVLFAIQQHNKQSA 300

Query: 301 A 301
           A
Sbjct: 301 A 301


Lambda     K      H
   0.318    0.135    0.395 

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: 531
Number of extensions: 9
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: 301
Length of database: 301
Length adjustment: 27
Effective length of query: 274
Effective length of database: 274
Effective search space:    75076
Effective search space used:    75076
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: 48 (23.1 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