Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate AO353_25125 AO353_25125 sugar ABC transporter permease
Query= TCDB::Q8RJU8 (307 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25125 Length = 280 Score = 146 bits (369), Expect = 5e-40 Identities = 86/264 (32%), Positives = 140/264 (53%), Gaps = 4/264 (1%) Query: 44 GILVLWAFMVVLPLLWAVMTSFKDDASIFGSPWSLPDKLHFDNWSRAWTEAHMGDYFLNT 103 GIL+L+A V P +A++TS K +++F + + D F N++ ++ N+ Sbjct: 20 GILLLYA---VFPFYYAIVTSLKPSSALFEVSYWI-DSPDFSNYAAVLHQSSFLRAIGNS 75 Query: 104 VLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVNNMG 163 ++V + L L AAY L R F G + + +G FP + L LF V+ +G Sbjct: 76 LVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQVAVLSGLFEVIRALG 135 Query: 164 LLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPMAKP 223 L NT LIL Y ++LPFTV+ LT F LP + EAA +DGAS T +++LP+ P Sbjct: 136 LYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLPLLWP 195 Query: 224 GLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLVMAM 283 L++ G+ F+ WN+++ +R + + ++ ++ W L A V+ Sbjct: 196 ALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHELPWGLLMAASVLVT 255 Query: 284 LPVLAAYIIFQRQVVQGLTAGALK 307 +P++ +IFQR++V GLTAGALK Sbjct: 256 VPLVILVLIFQRRIVSGLTAGALK 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: 261 Number of extensions: 18 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