Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate BPHYT_RS05035 BPHYT_RS05035 sugar ABC transporter permease
Query= TCDB::Q8RJU8 (307 letters) >FitnessBrowser__BFirm:BPHYT_RS05035 Length = 285 Score = 131 bits (329), Expect = 2e-35 Identities = 85/280 (30%), Positives = 142/280 (50%), Gaps = 9/280 (3%) Query: 36 TVLNVFSHGILVLWAFMVVLPLLWAVMTSFKD-DASIFGSPWSLPDKLHFDNWSRAWTEA 94 T+ + L L+A + PL + TSFKD D G+ + P D W +AW+ A Sbjct: 6 TISRAVIYAALFLFALYFLFPLYVMLSTSFKDIDQLRTGNLLTPPTHWTIDPWIKAWSGA 65 Query: 95 HMG-------DYFLNTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFP 147 G +F+N+V +V +++ + ++G+ YVL + F G I+ + + G P Sbjct: 66 CTGVRCDGMQPFFMNSVRMVIPAVLISSIIGAFNGYVLTHWRFRGADPIFTMILVGCFIP 125 Query: 148 IMLALVPLFYVVNNMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGA 207 L+P+ +GL NT GL++V++ Y + FT F F+ ++P+ + +AA +DGA Sbjct: 126 FQAILLPMARFEGFLGLSNTTTGLVVVHVIYGIAFTTMFFRNFYVSIPAELVKAARIDGA 185 Query: 208 SHTRTFFQIMLPMAKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQG 267 F +I+LP++ P + I+ F WN ++ V + D +T L L + Sbjct: 186 GFFTIFTKILLPVSLPIFMVCLIWQFTQIWNDFLFGIVF-SGVDSMPITVALNNLVNTST 244 Query: 268 YKGDWSGLFAGLVMAMLPVLAAYIIFQRQVVQGLTAGALK 307 +++ AG ++A LP L YII R V+GLTAGA+K Sbjct: 245 GVKEYNVDMAGAIIAALPTLLVYIIAGRYFVRGLTAGAVK 284 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: 285 Number of extensions: 25 Number of successful extensions: 3 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: 285 Length adjustment: 26 Effective length of query: 281 Effective length of database: 259 Effective search space: 72779 Effective search space used: 72779 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