Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate WP_110804641.1 C8J30_RS05120 hypothetical protein
Query= reanno::Smeli:SMc02875 (294 letters) >NCBI__GCF_003217355.1:WP_110804641.1 Length = 493 Score = 139 bits (349), Expect = 2e-37 Identities = 97/277 (35%), Positives = 143/277 (51%), Gaps = 14/277 (5%) Query: 6 IGIDGGGTSCRAAVAALDGRILGRGKAGAANILTDPETALQNITDAARDAFGDAGLDPAG 65 + IDGGG+ CRAA+ G+ L R + G ANI +D +TAL ++ + A GD LD Sbjct: 223 LAIDGGGSGCRAALCDDAGQELARAEGGPANIASDFDTALASLRELALRMIGDRPLDQV- 281 Query: 66 IGASRAIVGVAGHNVGDAVHYVKRRLPFAQADIESDGLIALQGALGDGDGAVAILGTGTI 125 RA++GVAG N+ A ++ LPF +A + D +L+GALGD DG +A +GTG++ Sbjct: 282 ----RAVLGVAGANLSGAGPRLEAALPF-RAKVVQDVTTSLRGALGDADGIMAAIGTGSV 336 Query: 126 YIARRGDEVSYVGGWGFTIGDHGSGARIGHALLQESLLAYDGIHQGSGVTDAVLAEFNDD 185 + + G EV +GGWGF +GD SGA +G +L DG S + AVL + Sbjct: 337 FARQVGGEVKAIGGWGFRLGDEASGAWMGRLMLNRITRMLDGYAPLSPLAKAVLDDLGGG 396 Query: 186 PRDIVDFARLAKPGEFGRYAPRVFEFAERGDPVAISLLKAAAATVDEALDVVVSRGSEKL 245 P +V F P + R+ E DP++ +L A + A+ ++ + + Sbjct: 397 P-GLVAFTLKKTPADHALLVHRMAAALE--DPLSRQVLTETRAELRAAIGLLQTDPPLPV 453 Query: 246 CLLGGLAPLYRRWLADRHQPRFVEARADALTGAVALA 282 LGGL P LA PR E +L GA+A+A Sbjct: 454 VWLGGLGPT----LALTDWPR-TEPLGSSLDGAMAMA 485 Lambda K H 0.320 0.139 0.410 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: 393 Number of extensions: 21 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: 294 Length of database: 493 Length adjustment: 30 Effective length of query: 264 Effective length of database: 463 Effective search space: 122232 Effective search space used: 122232 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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