Align citrate transporter (characterized)
to candidate Ga0059261_3091 Ga0059261_3091 Sugar (and other) transporter
Query= CharProtDB::CH_014606 (431 letters) >FitnessBrowser__Korea:Ga0059261_3091 Length = 430 Score = 227 bits (578), Expect = 6e-64 Identities = 132/389 (33%), Positives = 208/389 (53%), Gaps = 17/389 (4%) Query: 1 MTQQPSRAGT---FGAILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFA 57 M + AGT +IL ++GN +E +D++ + + Y A FFP + L+ T A Sbjct: 1 MNESSGEAGTRQRLKSILGGSAGNLVEWYDWYAYAAFTLYFAPHFFPKGDQTTQLLNTAA 60 Query: 58 VFGSGFLMRPIGAVVLGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLV 117 VF GFLMRPIG ++G Y D+ GR+ GL +++++M G+LLIA+ PGY+TIG LAP L+ Sbjct: 61 VFAVGFLMRPIGGWLMGVYADKYGRKAGLTLSVSLMCAGSLLIAVTPGYETIGALAPALL 120 Query: 118 LVGRLLQGFSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYG----L 173 + RL+QG S G E G + YLSE+A +GF++S+Q V ++ LI G L Sbjct: 121 VFARLMQGLSIGGEYGASATYLSEMAGRKRRGFFSSFQ----YVTLISGQLIALGVLLIL 176 Query: 174 NVTLGHDEISEWGWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIAKN 233 ++ + WGWRIPFFIG + ++F LRR L ET++F K + ++ Sbjct: 177 QASMSEAALESWGWRIPFFIGGALAVIVFWLRRGLSETQSFENAKAEGRKTGALALLREH 236 Query: 234 WRIITAGTLLVAMTTTTFYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWL---PI 290 L A T FY ++Y + ++N S D + + + F+++ P+ Sbjct: 237 PGEFLLVMALTAGGTLAFYAYSIYLQKF---LVNTSGFDRETASEINAAALFVFMCIQPL 293 Query: 291 GGAISDRIGRRPVLMGITLLALVTTLPVMNWLTAAPDFTRMTLVLLWFSFFFGMYNGAMV 350 GA+SDRIGR+P+++G +L ++ T P+ L ++L Y Sbjct: 294 AGALSDRIGRKPLMIGFGVLGVLCTYPIFTALEQVSSAWAAFGLMLGALVIVTGYTSINA 353 Query: 351 AALTEVMPVYVRTVGFSLAFSLATAIFGG 379 E+ P ++RT+G +L ++LA AIFGG Sbjct: 354 VVKAELFPAHIRTLGVALPYALANAIFGG 382 Lambda K H 0.328 0.141 0.432 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: 520 Number of extensions: 24 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: 431 Length of database: 430 Length adjustment: 32 Effective length of query: 399 Effective length of database: 398 Effective search space: 158802 Effective search space used: 158802 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: 51 (24.3 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