Align GtsC (GLcG), component of Glucose porter, GtsABCD (characterized)
to candidate HSERO_RS22745 HSERO_RS22745 sugar ABC transporter permease
Query= TCDB::Q88P36 (281 letters) >FitnessBrowser__HerbieS:HSERO_RS22745 Length = 300 Score = 129 bits (325), Expect = 6e-35 Identities = 81/268 (30%), Positives = 134/268 (50%), Gaps = 6/268 (2%) Query: 17 IHAVLLIAVLLYLVPLVVMLLTSFKTPEDITTGNL-LSWPAVITGIGWVKAWGAVSG--Y 73 +H VL + ++ L P+ ++L+ S KT I G + L +T G+ K Y Sbjct: 35 VHTVLCLYAVIALFPIALILINSVKTRNAIFEGPMALPTAETLTFAGFQKVLAGTHFLLY 94 Query: 74 FWNSIMITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTL 133 F NS+ +TV A+ + GA+ + L+ +RF G++ + G +P + + + Sbjct: 95 FGNSLAVTVAALFLIVLFGAMAAWALTEYRFFGNRALNFFIAIGIMIPIRLGTVSILQLV 154 Query: 134 GKLGLASTTGGLVLVHVVYGLAFTTLFFRNFYVSIPDALVKAARLDGAGFFTIFRRIILP 193 L L +T LVLV+ GL + F IP L AAR DG G +IF R+ILP Sbjct: 155 VALDLINTRTALVLVYTAQGLPLAVMILSEFMRQIPGELKDAARCDGVGELSIFFRVILP 214 Query: 194 MSTPIIMVCLIWQFTQIWNDFLFGVVFSSG-DSQPITVALNNLVNTSTGAKEYNVDMAAA 252 + P I ++ WND F ++ + G D++ +T+ + + A ++N +AA Sbjct: 215 LLRPAIATVAVFTMIPAWNDLWFPLILAPGEDTRTVTLGVQQFIGQY--ATDWNSVLAAL 272 Query: 253 MIAGLPTLLVYVVAGKYFVRGLTAGAVK 280 +A +P LL+Y+ + +RGLT+GAVK Sbjct: 273 SMAVIPVLLLYMAFSRQLIRGLTSGAVK 300 Lambda K H 0.329 0.142 0.443 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: 186 Number of extensions: 8 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: 281 Length of database: 300 Length adjustment: 26 Effective length of query: 255 Effective length of database: 274 Effective search space: 69870 Effective search space used: 69870 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 (21.8 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