Align GtsC (GLcG), component of Glucose porter, GtsABCD (characterized)
to candidate WP_084545369.1 H566_RS0118535 carbohydrate ABC transporter permease
Query= TCDB::Q88P36 (281 letters) >NCBI__GCF_000482785.1:WP_084545369.1 Length = 261 Score = 381 bits (979), Expect = e-111 Identities = 188/261 (72%), Positives = 214/261 (81%), Gaps = 9/261 (3%) Query: 30 VPLVVMLLTSFKTPEDITTGNLLSWPAVITGIGWVKAWGA---------VSGYFWNSIMI 80 +PL VML TSFKT ++I GNLLS PA + W KAW + + GYFWNS+ Sbjct: 1 MPLYVMLSTSFKTADEIRAGNLLSLPAQLDLHAWSKAWSSACTGSTCDGMRGYFWNSVSF 60 Query: 81 TVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTLGKLGLAS 140 VP+VLIST +GA NGYVL+MWRFRGS FGLL+ GCF+PFQ VLLP + TLG LG+AS Sbjct: 61 VVPSVLISTLMGAFNGYVLTMWRFRGSDTLFGLLMIGCFIPFQVVLLPMARTLGALGIAS 120 Query: 141 TTGGLVLVHVVYGLAFTTLFFRNFYVSIPDALVKAARLDGAGFFTIFRRIILPMSTPIIM 200 TTGGL+ VHVVYGLAFTTLFFRN+YV+IPD LVKAA++DGAGFF IFRRI LP+S PI + Sbjct: 121 TTGGLIFVHVVYGLAFTTLFFRNYYVTIPDELVKAAKIDGAGFFLIFRRITLPLSVPIFV 180 Query: 201 VCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVNTSTGAKEYNVDMAAAMIAGLPTL 260 V +IWQFTQ+WNDFLFGVVFSSG+ QPITVALNNLVNTSTG KEY+VDMAAA+IA LPTL Sbjct: 181 VSVIWQFTQVWNDFLFGVVFSSGERQPITVALNNLVNTSTGVKEYDVDMAAAIIAALPTL 240 Query: 261 LVYVVAGKYFVRGLTAGAVKG 281 VYVVAGKYFVRGLTAGAVKG Sbjct: 241 FVYVVAGKYFVRGLTAGAVKG 261 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: 284 Number of extensions: 8 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: 261 Length adjustment: 25 Effective length of query: 256 Effective length of database: 236 Effective search space: 60416 Effective search space used: 60416 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 24 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