Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate AO356_28580 AO356_28580 sugar ABC transporter permease
Query= TCDB::Q8RJU8 (307 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28580 Length = 280 Score = 145 bits (365), Expect = 1e-39 Identities = 85/263 (32%), Positives = 140/263 (53%), Gaps = 4/263 (1%) Query: 45 ILVLWAFMVVLPLLWAVMTSFKDDASIFGSPWSLPDKLHFDNWSRAWTEAHMGDYFLNTV 104 IL+++A V P +A++TS K +++F + + D+ F N++ +A N++ Sbjct: 21 ILLVYA---VFPFYYAIVTSLKPSSALFQVSYWI-DQPDFSNYAAVLNQASFLRAIGNSL 76 Query: 105 LVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVNNMGL 164 +V + L L AAY L R F G + + +G FP + L LF V+ +GL Sbjct: 77 VVALCVVALALFLSLTAAYALGRVKFRGRGPVLMMVLGVSMFPQVAVLSGLFEVIRALGL 136 Query: 165 LNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPMAKPG 224 NT LIL Y ++LPFTV+ LT F LP + EAA +DGAS T +++LP+ P Sbjct: 137 YNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLPLLWPA 196 Query: 225 LISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLVMAML 284 L++ G+ F+ WN+++ +R + + ++ ++ W L A V+ + Sbjct: 197 LVTTGLLAFIAAWNEFLFALTFTLTDSQRTVPVAIALISGGSPHELPWGLLMAASVLVTV 256 Query: 285 PVLAAYIIFQRQVVQGLTAGALK 307 P++ +IFQR++V GLTAGALK Sbjct: 257 PLVILVLIFQRRIVSGLTAGALK 279 Lambda K H 0.326 0.141 0.440 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: 256 Number of extensions: 17 Number of successful extensions: 1 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: 307 Length of database: 280 Length adjustment: 26 Effective length of query: 281 Effective length of database: 254 Effective search space: 71374 Effective search space used: 71374 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 (21.6 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