Align GtsC (GLcG), component of Glucose porter, GtsABCD (characterized)
to candidate SMc01979 SMc01979 sugar transport system permease ABC transporter protein
Query= TCDB::Q88P36 (281 letters) >FitnessBrowser__Smeli:SMc01979 Length = 277 Score = 140 bits (354), Expect = 2e-38 Identities = 87/267 (32%), Positives = 145/267 (54%), Gaps = 4/267 (1%) Query: 18 HAVLLIAVLLYLVPLVVMLLTSFKTPEDIT-TGNLLSWP--AVITGIGWVKAWGAVSGYF 74 H + ++A + + + + LL TP D+ + + WP A + +V A +F Sbjct: 12 HRLAVLAYIAFALFPLFWLLKVAVTPNDLLYSEGIRLWPSRASLEHFDFVLRHSAFPVFF 71 Query: 75 WNSIMITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTLG 134 NS++++ +I T + +L+GY LS +RFRG L+L P ++ P L Sbjct: 72 RNSLIVSGSTAVIVTILASLSGYALSRFRFRGKYWLVTLMLLTQMFPLVMLVAPIFKILS 131 Query: 135 KLGLASTTGGLVLVHVVYGLAFTTLFFRNFYVSIPDALVKAARLDGAGFFTIFRRIILPM 194 LGL ++ GLV+V+ + + F T ++F+ IP L +AA +DGA F FR+IILP+ Sbjct: 132 PLGLTNSLTGLVVVYTAFNVPFATFLMQSFFDGIPKDLEEAAMIDGATQFVAFRQIILPL 191 Query: 195 STPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVNTSTGAKEYNVDMAAAMI 254 + P I L + FT W++ LF ++ SG++Q T + L S + ++ MAA ++ Sbjct: 192 TLPGIAATLGFVFTAAWSELLFSLMLISGNAQ-ATFPVGLLSFVSKFSVDFGQMMAAGVL 250 Query: 255 AGLPTLLVYVVAGKYFVRGLTAGAVKG 281 A +P L +++ +Y V+GLTAGAVKG Sbjct: 251 ALIPACLFFLLIQRYLVQGLTAGAVKG 277 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: 9 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: 281 Length of database: 277 Length adjustment: 26 Effective length of query: 255 Effective length of database: 251 Effective search space: 64005 Effective search space used: 64005 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: 47 (22.7 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