Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate AZOBR_RS25590 AZOBR_RS25590 sugar ABC transporter permease
Query= TCDB::Q8RJU8 (307 letters) >FitnessBrowser__azobra:AZOBR_RS25590 Length = 277 Score = 156 bits (394), Expect = 6e-43 Identities = 85/263 (32%), Positives = 139/263 (52%), Gaps = 6/263 (2%) Query: 46 LVLWAFMVVLPLLWAVMTSFKDDASIFG-SPWSLPDKLHFDNWSRAWTEAHMGDYFLNTV 104 +V WA V P WA++TS K +++F W P + N++ + E G LN++ Sbjct: 19 IVAWA---VFPFAWAIVTSLKAGSALFTVEAW--PSQPSLANYAAIFKEQPFGRNILNSL 73 Query: 105 LVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVNNMGL 164 L + +L L +AAY L R F G + ++ +G FP + L LF +V +GL Sbjct: 74 LAASAVVALSLGLAVLAAYALGRVRFRGRGLLLFVVLGVSMFPQVAVLSGLFELVRWLGL 133 Query: 165 LNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPMAKPG 224 N + L+L Y+ ++LPFTV+ LT F R LP + EAA VDGA ++ LP+ P Sbjct: 134 YNRIGSLVLSYLIFTLPFTVWVLTTFMRELPKELEEAAMVDGAGPFVIVTRVFLPLMGPA 193 Query: 225 LISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLVMAML 284 L + G+ F+ WN+++ D R + + ++ + Y+ W + A V+ + Sbjct: 194 LAATGLLAFIAAWNEFLFALTFTLTDDARTVPVAIALMSGASQYELPWGQIMAASVVVTV 253 Query: 285 PVLAAYIIFQRQVVQGLTAGALK 307 P++ ++FQR++V GLTAGA+K Sbjct: 254 PLIGLVLLFQRRIVSGLTAGAVK 276 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: 263 Number of extensions: 15 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: 277 Length adjustment: 26 Effective length of query: 281 Effective length of database: 251 Effective search space: 70531 Effective search space used: 70531 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