Align GtsC (GLcG), component of Glucose porter, GtsABCD (characterized)
to candidate HSERO_RS01335 HSERO_RS01335 sugar ABC transporter permease
Query= TCDB::Q88P36 (281 letters) >FitnessBrowser__HerbieS:HSERO_RS01335 Length = 283 Score = 178 bits (451), Expect = 1e-49 Identities = 94/274 (34%), Positives = 162/274 (59%), Gaps = 6/274 (2%) Query: 12 LSRMAIHAVLLIAVLLYLVPLVVMLLTSFKTPEDITTGNLLSWP---AVITGIGWVKAWG 68 ++R A L +A+L++L+P++ L+TS ++ +++ GN WP A++ Sbjct: 12 INRALYRASLPVALLIWLLPMLAALVTSIRSNDELMAGNYWGWPQDFAMLENYREALTAS 71 Query: 69 AVSGYFWNSIMITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLP 128 + YFWNS +IT+P+V+ + ++ A+ G+ LS ++FRG+ + F + F+P Q +++P Sbjct: 72 PMLHYFWNSCLITIPSVIGAISLAAMAGFALSTYQFRGNTVLFATFVACNFVPQQILMIP 131 Query: 129 ASFTLGKLGLASTTGGLVLVHVVYGLAFTTLFFRNFYVSIPDALVKAARLDGAGFFTIFR 188 LGL +T G++L H+ F TLF RNF +P +++AAR++GA +T+F Sbjct: 132 VRDLSLSLGLFNTITGMMLFHIAMQTGFCTLFLRNFIKQLPFEMIEAARIEGASEWTVFY 191 Query: 189 RIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDS-QPITVALNNLVNTSTGAKEYNV 247 RI+LP+ P + + FT +WND+ + +V + GD PITV + L T A +N+ Sbjct: 192 RIVLPLIRPALAALAVLVFTFVWNDYFWALVLTQGDDVAPITVGVAALRGQWTTA--WNL 249 Query: 248 DMAAAMIAGLPTLLVYVVAGKYFVRGLTAGAVKG 281 A +++A LP+++++ V K FV GLT GA KG Sbjct: 250 VSAGSILAALPSVILFFVMQKQFVAGLTFGASKG 283 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: 225 Number of extensions: 13 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: 283 Length adjustment: 26 Effective length of query: 255 Effective length of database: 257 Effective search space: 65535 Effective search space used: 65535 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