Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate 7023652 Shewana3_0881 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::P48244 (228 letters) >FitnessBrowser__ANA3:7023652 Length = 226 Score = 80.5 bits (197), Expect = 2e-20 Identities = 61/217 (28%), Positives = 101/217 (46%), Gaps = 22/217 (10%) Query: 12 LLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVLFC 71 +L VT+ +T ++ + + G T M++S +R + Y+ +R TP+ + ++ Sbjct: 24 ILNGLKVTLIVTFFAMLLGAVLGVGTTLMKMSSKWYIRFPAELYVGVIRGTPVVVQLVIL 83 Query: 72 SFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTVHFGQAEAA 131 F + LA F VD A++ F L + +++E +R+GI V GQ EAA Sbjct: 84 YF-------IVLAA-----FDVDK-VTAAIIAFGLNSGAYISEIIRAGIQAVDKGQTEAA 130 Query: 132 RSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIG----VGEASLLMKAT 187 RSLGL T + II PQA++ + LGN I L K T + IG + ++ T Sbjct: 131 RSLGLSQAMTMKLIILPQAIKNILPALGNEFIVLLKETAVIGFIGGVDLMRAGEIIRSRT 190 Query: 188 IENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERL 224 E+ + A+ ++ LT L K +RL Sbjct: 191 FEDS-----IPLFTCALIYLFLTYSFTFMLSKFEKRL 222 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: 146 Number of extensions: 10 Number of successful extensions: 1 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: 226 Length adjustment: 22 Effective length of query: 206 Effective length of database: 204 Effective search space: 42024 Effective search space used: 42024 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