Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate RR42_RS31740 RR42_RS31740 ABC transporter permease
Query= TCDB::P48244 (228 letters) >FitnessBrowser__Cup4G11:RR42_RS31740 Length = 222 Score = 101 bits (251), Expect = 1e-26 Identities = 72/224 (32%), Positives = 115/224 (51%), Gaps = 15/224 (6%) Query: 2 STLWADLGPSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVK-ILRTLSTAYINTVR 60 S +WA P L+ VT+++T + + + G ++ R+ P + ++ L TAY+ +R Sbjct: 6 SPVWAGW-PDLVRGAGVTVEVTACALVLGCVMGLLVGIGRLDPRRRVVYGLCTAYVTAIR 64 Query: 61 NTPLTLVVLFCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGI 120 TPL + + FGL Q L A F V+G +Y+ +V+E +R I Sbjct: 65 GTPLLVQLFLLFFGLPQFDILLPA------------FVCGVIGLGIYSGAYVSEIVRGAI 112 Query: 121 NTVHFGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEA 180 +V GQ EAARS+G+ G R++I PQA+ I PLGN IAL KN+ + S++ + + Sbjct: 113 QSVDKGQMEAARSIGMSSGQAMRAVILPQAIVRMIPPLGNEFIALIKNSALVSLLTIHDV 172 Query: 181 SLLMKATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERL 224 + I L V AI A+ +++LT GL L + +RL Sbjct: 173 MHEGQKIISVSYRSLEVYLAI-ALVYLLLTSAAGLFLRHMEQRL 215 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: 139 Number of extensions: 4 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: 222 Length adjustment: 22 Effective length of query: 206 Effective length of database: 200 Effective search space: 41200 Effective search space used: 41200 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