Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate SM_b20232 SM_b20232 sugar ABC transporter permease
Query= TCDB::Q8RJU9 (308 letters) >FitnessBrowser__Smeli:SM_b20232 Length = 314 Score = 142 bits (358), Expect = 1e-38 Identities = 104/303 (34%), Positives = 163/303 (53%), Gaps = 38/303 (12%) Query: 8 FIVGFLAV---PLGLYALLVVWPFIQSIYYSFTDWTGLSPDFKTVGFDNYERMLDDDIFW 64 +I G+L V LGL+ L V P S+ S + G + VG NY RM +D +FW Sbjct: 26 WIAGYLFVLPDALGLFIFLGV-PMALSLVLSVFEVNGFG-GYSFVGARNYLRMWNDPLFW 83 Query: 65 KSLQHSLLFAL----LLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIVYFF 120 K + + L+A LL V +GLAL V R + + ++F Sbjct: 84 KGARVTALYAAMLVPLLYVCGLGLALL----------------VQRTDRFNAIMRSMFFA 127 Query: 121 PQVLSIAIVALLFAFAYNPDSGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVWSTV 180 P ++S+ +VAL++ F G ++ L + +G + LGDP+ AL ++ V VW + Sbjct: 128 PHMVSLVVVALVWQFMVVDKIGVVSRLTAALDIGGIS--LLGDPNFALITIVLVSVWFLM 185 Query: 181 GFFVVLFSAGMASIPADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGIL---AL 237 GF++++F G+ IP YEAA++DGA + F+ ITLPLL T S +V M + Sbjct: 186 GFYMLIFLGGLQDIPRQYYEAAMIDGAGAIARFWFITLPLLKPT--SFFVIMVSMVAAVA 243 Query: 238 GAESFAVVHIMTTGPGGPDYSTTVMVLYVYQKAFRDG----QAAYATTIGVALLIVTLAF 293 GA++F ++++MT GGP +T+V+++Y+YQ+AF G AA A+ + VAL+IVT F Sbjct: 244 GAQAFDIIYVMT--KGGPANATSVLIVYIYQQAFGFGAFGYAAAMASILVVALMIVTAVF 301 Query: 294 AAV 296 A+ Sbjct: 302 FAL 304 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: 286 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 308 Length of database: 314 Length adjustment: 27 Effective length of query: 281 Effective length of database: 287 Effective search space: 80647 Effective search space used: 80647 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