Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate Synpcc7942_0949 Synpcc7942_0949 permease protein of sugar ABC transporter
Query= TCDB::Q8RJU9 (308 letters) >FitnessBrowser__SynE:Synpcc7942_0949 Length = 292 Score = 121 bits (304), Expect = 2e-32 Identities = 92/294 (31%), Positives = 138/294 (46%), Gaps = 26/294 (8%) Query: 9 IVGFLAVPLGLYALLVVWPFIQSIYYSFTDWTGLSPDFKTVGFDNYERMLDDDIFWKSLQ 68 I G A PL L W +Q++ + T L P F +G NY+R+ D FW L Sbjct: 16 ITGVFAYPL----LRAAWLSLQALNLN----TQLQPVF--IGLANYQRLWGDSRFWGDLF 65 Query: 69 HSLLFALLLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIVYFFPQVLSIAI 128 ++ +F + + + L L A +++ R R GP+ T + P VL A+ Sbjct: 66 NTTVFTVTSVSLELVLGLAIALLLHQPSRWR--GPLRT----------IALLPWVLPTAV 113 Query: 129 VALLFAFAYNPDSGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVWSTVGFFVVLFS 188 +AL +A+ +N G N L+ +G WLG+P A ++A VW T F +L Sbjct: 114 MALGWAWIFNDPYGVWNDWLQQLGWIAAPINWLGNPRWAWLTLVAADVWKTTPFVAILLL 173 Query: 189 AGMASIPADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILALGAESFAVVHIM 248 AG +IP D+YEA L+GA +F++ITLPLL + ++ A G F +V +M Sbjct: 174 AGRQAIPEDLYEAHCLEGATAWQSFWQITLPLLRPQLAIALLFRSAQAFGL--FDLVKVM 231 Query: 249 TTGPGGPDYSTTVMVLYVYQKAFRDGQAAYATTIGVALLIVTLAFAAVVMRLGR 302 T GGP ST + LY Y A R Y T+ + + A ++ LGR Sbjct: 232 T--GGGPANSTETLALYAYTTALRYLDFGYGATLAIVTAAILAAGLGLIWGLGR 283 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: 289 Number of extensions: 14 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: 292 Length adjustment: 27 Effective length of query: 281 Effective length of database: 265 Effective search space: 74465 Effective search space used: 74465 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