Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate BPHYT_RS19060 BPHYT_RS19060 ATPase
Query= reanno::MR1:202608 (300 letters) >FitnessBrowser__BFirm:BPHYT_RS19060 Length = 293 Score = 130 bits (327), Expect = 4e-35 Identities = 93/290 (32%), Positives = 139/290 (47%), Gaps = 6/290 (2%) Query: 7 NDQQLFIGVDGGGSKCRATIYTADGTVLGTGVAGRANPLHGLAQTFESIEASAHQALLDA 66 N IG+DGGGS R + A G L +G + G+ + +++I A +A A Sbjct: 2 NKDFFLIGIDGGGSGTRVVLGDAQGRELAQAASGPSGLGLGVERAWQAIAAGCGEAFASA 61 Query: 67 GMKATDSHLLVAGLGLAGVNVPRLYQDVVNWQHP-FAAMYVTTDLHTACIGAHRGADGAV 125 G KA D V G GLAGVN R + Q P A + V +D +T +GAH GA G + Sbjct: 62 G-KALDWSRCVLGCGLAGVN-NRDWLAAFRAQAPALAGLAVESDAYTTLLGAHGGAHGVI 119 Query: 126 IITGTGSCGYAHVGDASL-SIGGHGFALGDKGSGAWLGLKAAEHVLLALDGFATPTALTE 184 + GTGS G+ + G+GF GD+ SGAWLGL+ H ALDG L Sbjct: 120 VALGTGSVAAVLDGEGECRQVSGYGFPSGDEASGAWLGLRVIVHAQQALDGRGPIDDLAR 179 Query: 185 MLLSHLGVKDALGIVEHLAGKSSSCYAQLARNVLDCANAGDQVAIAIVQEGADYISEMAR 244 L++H G D +V L + + YA+LA ++ A+ A ++ E + +M Sbjct: 180 ALVAHTGAHDRDSLVVWLCEANQTAYARLAPILI--AHRTHPFAARLLGEAGAEVGKMIT 237 Query: 245 KLFMLNPVRFSMIGGLAEPLQAWLGSDVVAKISETLAPPELGAMYYAQQQ 294 L + ++ GGL PL+ ++ A++ E LA G + AQ++ Sbjct: 238 ALDPSASLPVALCGGLGAPLREYVPQIYQARLREPLADSAHGGLQLAQRE 287 Lambda K H 0.319 0.135 0.400 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: 299 Number of extensions: 18 Number of successful extensions: 4 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: 300 Length of database: 293 Length adjustment: 26 Effective length of query: 274 Effective length of database: 267 Effective search space: 73158 Effective search space used: 73158 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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