Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate WP_015888140.1 NGR_RS09950 sugar ABC transporter permease
Query= TCDB::Q8RJU9 (308 letters) >NCBI__GCF_000018545.1:WP_015888140.1 Length = 307 Score = 121 bits (303), Expect = 2e-32 Identities = 91/302 (30%), Positives = 149/302 (49%), Gaps = 22/302 (7%) Query: 1 MQHGKYRFIVGFLAVPLGLYAL-LVVWPFIQSIYYSFTDWTGLSPD--FKTVGFDNYERM 57 ++H R + + P L L L ++P I ++Y+ +PD ++ VG N+ R+ Sbjct: 19 LEHWAERHLRYLMLAPTVLILLALTIFPSIY-MFYAAVHRISPNPDLPWEFVGVGNFARL 77 Query: 58 LDDDIFWKSLQHSLLFALLLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIV 117 L D F +L+++++F L+ + L L A +++ +R F K V Sbjct: 78 LSDPQFHVALRNTVVFTLVAVALEFLLGLGLALLLD------------RFIRRLSFLKTV 125 Query: 118 YFFPQVLSIAIVALLFAFAYNPDSGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVW 177 P +L VA+ + Y P G +N ++ +GL VQ W GD +LA++ ++ VW Sbjct: 126 LMIPMMLPPIAVAITWKLIYEPQFGVLNEIMFLLGL-PVQ-AWAGDVNLAMFSIIVADVW 183 Query: 178 STVGFFVVLFSAGMASIPADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILAL 237 F +L AG+AS+P + YEAA LDGA+ F+ +TLP L + + + AL Sbjct: 184 QWTPFVFLLMLAGLASLPVEPYEAAALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDAL 243 Query: 238 GAESFAVVHIMTTGPGGPDYSTTVMVLYVYQKAFRDGQAAYATTIGVALLIVTLAFAAVV 297 F +V I+T GGP T V+ LY+YQ A+R YA I + +L VT+ + Sbjct: 244 --RLFDLVFILT--GGGPADRTKVLSLYIYQVAYRFADPGYAAAISLFVLFVTIVLSTWF 299 Query: 298 MR 299 M+ Sbjct: 300 MK 301 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: 245 Number of extensions: 12 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: 307 Length adjustment: 27 Effective length of query: 281 Effective length of database: 280 Effective search space: 78680 Effective search space used: 78680 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 Apr 09 2024. 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