Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate AZOBR_RS25585 AZOBR_RS25585 ABC transporter permease
Query= TCDB::Q8RJU9 (308 letters) >FitnessBrowser__azobra:AZOBR_RS25585 Length = 301 Score = 129 bits (323), Expect = 1e-34 Identities = 82/292 (28%), Positives = 144/292 (49%), Gaps = 19/292 (6%) Query: 12 FLAVPLGLYALLVVWPFIQSIYYSFTDWTGLSPD-FKTVGFDNYERMLDDDIFWKSLQHS 70 FL L + A + WP +++++SFTD T + + F+ VG DNY ++ D ++W+++ ++ Sbjct: 21 FLLPMLIVLAGVAGWPLFRTVFFSFTDATLATLEGFQGVGLDNYLWLMRDPVWWRAVWNT 80 Query: 71 LLFALLLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIVYFFPQVLSIAIVA 130 L+F ++ + L L A ++N + G G + P + + A Sbjct: 81 LVFTVVSVGIETALGLGIALILNAH------------LPGRGLLRAAVLIPWAIPTVVSA 128 Query: 131 LLFAFAYNPDSGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVWSTVGFFVVLFSAG 190 ++ + ++ G +N++L G+GL W DPDLAL V+AV VW + F +L A Sbjct: 129 QMWGWMFHDLYGVVNAILMGLGLIAEPRAWTADPDLALPVVIAVDVWKSTPFMALLILAA 188 Query: 191 MASIPADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILALGAESFAVVHIMTT 250 + +P D+YEAA +DG + V F RITLPL+ + ++ + AL F +++++T Sbjct: 189 LQMLPRDLYEAARVDGVHPVKVFVRITLPLIRPALMVAVLFRTLDAL--RVFDLMYVLT- 245 Query: 251 GPGGPDYSTTVMVLYVYQKAFRDGQAAYATTIGVALLIVTLAFAAVVMRLGR 302 G ST M +Y Q Y + L++V + + LGR Sbjct: 246 ---GNSRSTMSMSVYARQYLIDFQDVGYGSAAATLLVLVLAVATVLAVTLGR 294 Lambda K H 0.330 0.145 0.458 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: 268 Number of extensions: 17 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: 308 Length of database: 301 Length adjustment: 27 Effective length of query: 281 Effective length of database: 274 Effective search space: 76994 Effective search space used: 76994 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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