Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate GFF3909 PGA1_65p00120 putative amino-acid ABC transporter, permease protein
Query= TCDB::P48244 (228 letters) >FitnessBrowser__Phaeo:GFF3909 Length = 224 Score = 89.0 bits (219), Expect = 7e-23 Identities = 68/219 (31%), Positives = 107/219 (48%), Gaps = 18/219 (8%) Query: 12 LLPAFWVTIKLTIYSAIGAMIFGTILTTM----RVSPVKILRTLSTAYINTVRNTPLTLV 67 L+P + LT++ A+ AM+ +L ++ RV + +L L +I+ R TPL + Sbjct: 12 LVPVLLSYVPLTLFMAVVAMVLALVLASLLAVERVLRIPVLDQLVVLFISFFRGTPLLVQ 71 Query: 68 VLFCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTVHFGQ 127 + +GL Q L S N A++G L+ + ++AES+R+ I V Q Sbjct: 72 LFLFYYGLPQVL---------SVLTQINGVSAAIMGLTLHFAAYMAESIRAAILGVDRSQ 122 Query: 128 AEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEASLLMKAT 187 EAA+S+G+ G R I+ PQA R A L N I + K T++A +GV E +M AT Sbjct: 123 WEAAQSIGMTRGQMMRRIVLPQAARIAAPTLVNYFIDMIKGTSLAFTLGVTE---MMGAT 179 Query: 188 IENHAN--MLFVVFAIFAVGFMILTLPMGLGLGKLSERL 224 + A + F F + AV + IL + L +L L Sbjct: 180 QKEAAGSFLYFEAFLVVAVIYWILVEALSLVQRRLETHL 218 Lambda K H 0.327 0.139 0.397 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: 119 Number of extensions: 5 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 228 Length of database: 224 Length adjustment: 22 Effective length of query: 206 Effective length of database: 202 Effective search space: 41612 Effective search space used: 41612 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 (21.7 bits) S2: 46 (22.3 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