Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate 6936101 Sama_0298 ATPase, BadF/BadG/BcrA/BcrD type (RefSeq)
Query= reanno::ANA3:7025966 (302 letters) >FitnessBrowser__SB2B:6936101 Length = 327 Score = 222 bits (566), Expect = 8e-63 Identities = 117/282 (41%), Positives = 176/282 (62%), Gaps = 4/282 (1%) Query: 12 FIGVDGGGSKCRATIYTADGTVLGTGVAGRANPLHGLAQTFASIEASTRQALLDAGMKET 71 ++G+D GGS CRA + G VLG GVAG ANP++G++Q+ A+I ++ +AL A + Sbjct: 39 WVGIDAGGSHCRALLTDDSGQVLGHGVAGPANPVNGVSQSQAAIMSAIDKAL-GAARLDK 97 Query: 72 DSHLLVAGLGLAGVNVPRLYQDVISWQHPFAAMYVTTDLHTACIGAHRGADGAVIITGTG 131 H L+ G GLAG+++P++ Q + W HPFAA + TTDLH A +GAH+GADG VII GTG Sbjct: 98 QYHRLIVGAGLAGLHLPKMQQVMNEWAHPFAAWHTTTDLHVAALGAHQGADGGVIILGTG 157 Query: 132 SCGYAHVGDDSLSIGGHGFALGDKGSGAWLGLKAAEHVLLALDGFATPTALTEMLLKHFG 191 A+V + IGGHGF + SG+W GL+A + VLL DG T+LT LL+ Sbjct: 158 FSSLANVKGQQILIGGHGFPINATCSGSWFGLEAVKAVLLDADGIGPGTSLTGKLLQG-- 215 Query: 192 VSDALGIVEHLAGKSSSCYAELARSVLDCANAGDEVARGIVQEGADYISEMARKLFSLNP 251 ++A+ + E L +++ +A A V + A AGD V+ ++++GA +I+ + R+L + Sbjct: 216 -TNAMALAEQLMHANATDFARFAPQVFEQAGAGDAVSLSLIEQGATFINGVIRRLLATGI 274 Query: 252 VRFSMIGGLAEPLQAWLGSDVVAKISETLAPPELGAMYFAQQ 293 S++GG+A +Q WL D+ +I A PE GA+ FA+Q Sbjct: 275 DSLSLVGGIAPLMQPWLAPDLSTRIRTAKASPEEGAILFARQ 316 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: 307 Number of extensions: 13 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: 302 Length of database: 327 Length adjustment: 27 Effective length of query: 275 Effective length of database: 300 Effective search space: 82500 Effective search space used: 82500 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 (21.7 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