Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate SM_b21105 SM_b21105 sugar ABC transporter permease
Query= TCDB::Q8RJU8 (307 letters) >FitnessBrowser__Smeli:SM_b21105 Length = 288 Score = 157 bits (396), Expect = 4e-43 Identities = 89/269 (33%), Positives = 143/269 (53%), Gaps = 10/269 (3%) Query: 46 LVLWAFMVVLPLLWAVMTSFKDDASIFGSP--WSLPDKLHFDNWSRAWTEAHMG-----D 98 L L ++ LP LW V++S + I P W +P+ L D + ++ A G D Sbjct: 22 LFLAMLVICLPGLWIVLSSLRPTVEIMAKPPVW-IPETLSLDAYRAMFSGAGQGGVPVWD 80 Query: 99 YFLNTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYV 158 YF N+++V S + L +G Y AR+ F I+ F+ + P + +PLF + Sbjct: 81 YFRNSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVPGIALSLPLFML 140 Query: 159 VNNMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIML 218 G+++T LIL Y+A ++PFT++ + FFR +P +AEAA +DG + + F+Q+ Sbjct: 141 YARTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCTPWQAFWQVEF 200 Query: 219 PMAKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAG 278 P+A PG+ S GIF FL WN+Y L + + + + L GL+ + DW G+ A Sbjct: 201 PLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAE--FTIDWRGMCAL 258 Query: 279 LVMAMLPVLAAYIIFQRQVVQGLTAGALK 307 V+ ++P L I Q+ +V GLT GA+K Sbjct: 259 AVVMIVPALTLTFIIQKHLVSGLTFGAVK 287 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: 215 Number of extensions: 7 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: 288 Length adjustment: 26 Effective length of query: 281 Effective length of database: 262 Effective search space: 73622 Effective search space used: 73622 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