Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate 6936757 Sama_0944 hypothetical protein (RefSeq)
Query= reanno::SB2B:6936757 (301 letters) >FitnessBrowser__SB2B:6936757 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.
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:
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