Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate WP_007665545.1 BN137_RS16135 carbohydrate ABC transporter permease
Query= TCDB::Q8RJU8 (307 letters) >NCBI__GCF_000319285.1:WP_007665545.1 Length = 281 Score = 154 bits (388), Expect = 3e-42 Identities = 80/254 (31%), Positives = 138/254 (54%), Gaps = 1/254 (0%) Query: 54 VLPLLWAVMTSFKDDASIFGSPWSLPDKLHFDNWSRAWTEAHMGDYFLNTVLVVGGSLIG 113 V P +A+++S ++ +F +P P H+DN+ A + + LN+VLV ++ Sbjct: 28 VFPFYYAIISSLREGQELF-TPAYFPTGWHWDNYVVALVDNGIARSLLNSVLVAAVTVGL 86 Query: 114 TLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVNNMGLLNTLHGLIL 173 L + AA+ LAR F G R + + + FP + L +F +V +GL ++L L++ Sbjct: 87 CLFVSVTAAFALARVPFRGRRVLLFTILCVSMFPQVAVLTGMFELVRFLGLYDSLGALVI 146 Query: 174 VYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPMAKPGLISVGIFNF 233 Y +SLPFTV+ LT F +++P + EAA VDGA +I P+ P +++ G+ F Sbjct: 147 SYTTFSLPFTVWVLTTFMKSIPVELEEAAIVDGAKTGTIIRRIFAPVLAPAMVTTGLLAF 206 Query: 234 LGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLVMAMLPVLAAYIIF 293 +G WN++M DKR + + + + Y+ W + A V+ LP++ +IF Sbjct: 207 IGAWNEFMFALTFIISGDKRTVPVAISLFSGASSYELPWGSIMAASVVVTLPIIVLVLIF 266 Query: 294 QRQVVQGLTAGALK 307 Q+++V GLT+GA+K Sbjct: 267 QKRIVSGLTSGAIK 280 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: 248 Number of extensions: 9 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: 281 Length adjustment: 26 Effective length of query: 281 Effective length of database: 255 Effective search space: 71655 Effective search space used: 71655 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 24 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