Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate GFF355 PS417_01810 ABC transporter permease
Query= TCDB::P48244 (228 letters) >FitnessBrowser__WCS417:GFF355 Length = 319 Score = 106 bits (265), Expect = 5e-28 Identities = 71/223 (31%), Positives = 110/223 (49%), Gaps = 20/223 (8%) Query: 5 WADLGPSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPL 64 WA LGP L+ W T+ L++ S I +I G R+S LR LST Y+ VR TPL Sbjct: 112 WA-LGP-LMWGLWTTLWLSVVSGILGLIIGLATGLCRLSSNPTLRDLSTIYVELVRGTPL 169 Query: 65 TLVVLFCSF--GLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINT 122 + + F G NL AG + L+T +VAE +R+G+ + Sbjct: 170 LVQIFIFYFFIGTVLNLSREFAG---------------IAALSLFTGAYVAEIVRAGVQS 214 Query: 123 VHFGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEASL 182 + GQ EAARSLGL + R ++ PQA + + PL I+L K+T++ SVI + E Sbjct: 215 ITRGQNEAARSLGLSASQSMRHVVLPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELLK 274 Query: 183 LMKATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERLA 225 + I + ++F + + ++++ LP+ +L RLA Sbjct: 275 SGREVITTSFSPFEILFCVAGL-YLLINLPLSKMASRLERRLA 316 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: 154 Number of extensions: 7 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: 228 Length of database: 319 Length adjustment: 25 Effective length of query: 203 Effective length of database: 294 Effective search space: 59682 Effective search space used: 59682 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: 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