Align GtsC (GLcG), component of Glucose porter, GtsABCD (characterized)
to candidate WP_086510783.1 BZY95_RS15420 carbohydrate ABC transporter permease
Query= TCDB::Q88P36 (281 letters) >NCBI__GCF_002151265.1:WP_086510783.1 Length = 292 Score = 378 bits (971), Expect = e-110 Identities = 190/279 (68%), Positives = 225/279 (80%), Gaps = 9/279 (3%) Query: 12 LSRMAIHAVLLIAVLLYLVPLVVMLLTSFKTPEDITTGNLLSWPAVITGIGWVKAWG--- 68 L R ++AVLL+A L YL+PL VML+TS K +IT G LLS P T W KAWG Sbjct: 14 LGRAMLYAVLLLAALFYLLPLAVMLITSVKPLAEITPGTLLSLPREPTLAPWGKAWGEAC 73 Query: 69 ------AVSGYFWNSIMITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPF 122 + YF+NSI I VPAVLISTAIGALNGY L+ WRF+GS+L F L+LFGCF+PF Sbjct: 74 TGMRCEGIGVYFFNSIAIVVPAVLISTAIGALNGYALTKWRFKGSELLFALMLFGCFIPF 133 Query: 123 QTVLLPASFTLGKLGLASTTGGLVLVHVVYGLAFTTLFFRNFYVSIPDALVKAARLDGAG 182 Q VLLP + TLG LGL+S+ GL+LVHV++G+AFTTLFFRNFYV++P LV AA+LDGAG Sbjct: 134 QVVLLPMAQTLGWLGLSSSRAGLILVHVIFGIAFTTLFFRNFYVAVPTELVSAAKLDGAG 193 Query: 183 FFTIFRRIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVNTSTGA 242 FF IF RI+LP+S PII+V +IWQFTQIWNDFLFGV FS+ ++QP+TVALNNLVNTSTGA Sbjct: 194 FFRIFWRILLPVSAPIIVVSVIWQFTQIWNDFLFGVAFSAHNTQPVTVALNNLVNTSTGA 253 Query: 243 KEYNVDMAAAMIAGLPTLLVYVVAGKYFVRGLTAGAVKG 281 +EYNVDMAAAMIA LPTL+VYV+AGKYFVRGLTAG+VKG Sbjct: 254 REYNVDMAAAMIAALPTLIVYVLAGKYFVRGLTAGSVKG 292 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: 268 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: 292 Length adjustment: 26 Effective length of query: 255 Effective length of database: 266 Effective search space: 67830 Effective search space used: 67830 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