Align Ribose import permease protein RbsC (characterized)
to candidate 3606962 Dshi_0389 Monosaccharide-transporting ATPase (RefSeq)
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Dino:3606962 Length = 357 Score = 178 bits (451), Expect = 2e-49 Identities = 113/324 (34%), Positives = 178/324 (54%), Gaps = 16/324 (4%) Query: 8 GRRYFTKAW---LMEQKSLIALLVLIAIVST----LSPNFFTINNLFNILQQTSVNAIMA 60 G + FT+ + L + +L+ L+VL+A ++ L FF+ L ILQQ + I+A Sbjct: 28 GPQGFTRKFQHALHQTPALVPLIVLVAAIAVFGLLLGSKFFSPFALTLILQQVQIVGIVA 87 Query: 61 VGMTLVILTSGIDLSVGSLLALTGAVAASIV---GIEVNALVAVAAALALGAAIGAVTGV 117 +LVILT+GIDLSVG+++ ++ V G+ V VAVA L G +G + G Sbjct: 88 AAQSLVILTAGIDLSVGAIMVMSSVVMGQFTFRYGLPVE--VAVACGLLCGTLLGFINGW 145 Query: 118 IVAKGRVQAFIATLVMMLLLRGVTMVYTNGSPVNT-GFTENADLFGWFGIGRPLG---VP 173 +VAK ++ FI TL M ++ +Y+ + + + A L +FG +G + Sbjct: 146 LVAKVKLPPFIVTLGMWQIVLAANFLYSRNETIRSQDIRDQAPLLQFFGTTLEIGGARLT 205 Query: 174 TPVWIMGIVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASL 233 V M ++ + Y L HT GR++YA+G + A LSG+ V++ I VY L GL+ + Sbjct: 206 YGVIFMVLLVIVLAYALRHTAWGRHVYAVGDDPEAAELSGVQVSRTLISVYMLSGLICAF 265 Query: 234 AGIIEVARLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLN 293 AG + R+ S PT+G +++I AVV+GG SL GG+G I+G GALI+G GL Sbjct: 266 AGWALIGRIGSVSPTSGQLANIESITAVVIGGISLFGGRGSILGAFFGALIVGVFTLGLR 325 Query: 294 LLGVSSYYQMIVKAVVILLAVLVD 317 LLG + + ++ ++I+ AV VD Sbjct: 326 LLGADAQWTFLLIGLLIIAAVAVD 349 Lambda K H 0.324 0.139 0.393 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: 252 Number of extensions: 10 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: 321 Length of database: 357 Length adjustment: 28 Effective length of query: 293 Effective length of database: 329 Effective search space: 96397 Effective search space used: 96397 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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