Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate 15432 b1312 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= TCDB::Q8RJU8 (307 letters) >FitnessBrowser__Keio:15432 Length = 280 Score = 132 bits (331), Expect = 1e-35 Identities = 82/265 (30%), Positives = 135/265 (50%), Gaps = 5/265 (1%) Query: 46 LVLWAFMVVLPLLWAVMTSFKD-DASIFGSPWSLPDKLHFDNWSRAWTEAHMG--DYFLN 102 L L+ + + P +MTSFK +I P LP + +++ + DYF N Sbjct: 17 LALFLIITLFPFFVMLMTSFKGAKEAISLHPTLLPQQWTLEHYVDIFNPMIFPFVDYFRN 76 Query: 103 TVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVNNM 162 +++V S + + LG + AY L+R F G I F F +L +VPLF ++ + Sbjct: 77 SLVVSVVSSVVAVFLGILGAYALSRLRFKGRMTINASFYTVYMFSGILLVVPLFKIITAL 136 Query: 163 GLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPMAK 222 G+ +T LI+ + +LP VF L ++F T+P + EAA +DG + + F+I +P+A Sbjct: 137 GIYDTEMALIITMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDGLNRLQIIFRITVPLAM 196 Query: 223 PGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLVMA 282 GLISV ++ F+ WN Y+ ++ + L GL L + Y W + A ++ Sbjct: 197 SGLISVFVYCFMVAWNDYLFASIFLSSASNFTLPVGLNALFSTPDY--IWGRMMAASLVT 254 Query: 283 MLPVLAAYIIFQRQVVQGLTAGALK 307 LPV+ Y + +R + GLTAG +K Sbjct: 255 ALPVVIMYALSERFIKSGLTAGGVK 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: 250 Number of extensions: 18 Number of successful extensions: 2 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