Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate BPHYT_RS24175 BPHYT_RS24175 C4-dicarboxylate ABC transporter
Query= SwissProt::Q9KQR9 (332 letters) >FitnessBrowser__BFirm:BPHYT_RS24175 Length = 330 Score = 157 bits (397), Expect = 3e-43 Identities = 96/317 (30%), Positives = 163/317 (51%), Gaps = 21/317 (6%) Query: 7 LIAASILAVTSFNAAANCDPGEIVIKFSHVTNTDKHPKGIAASLLEKRVNEEMNGKACMQ 66 ++AAS+LA+++ +A A V + S V + D +P +A + + +N+ GK ++ Sbjct: 13 IVAASVLALSTVSAQAR------VFRVSDV-HGDTYPTNMAVKHMGEEINKATGGKDSVK 65 Query: 67 VFPNSTLYDDDKVLEALLNGDVQLAAPSLSKFEKFTKKYRIFDLPFLFEDVDAVDRFQSS 126 VF NS L ++ ++ + G + +A + + F + + I LPFLF D+D + Sbjct: 66 VFGNSALGSENDTIDQVRIGALDMARANGAAFNEIVPESMIPSLPFLFRDIDHFRKVMYG 125 Query: 127 AKGEELKNAMTRRGVKGLEFWHNGMKQISANKPILVPADAKGLKFRVQASDVLVAQFEQI 186 +G+++ +A +G+ L F+ +G + I KPI PAD KGLK RVQ SD++V + + Sbjct: 126 PEGQKILDAFKAKGMIALTFYESGARSIYTKKPIHTPADMKGLKVRVQPSDLMVDEIRAM 185 Query: 187 GANPQKMSFAETYGGLQTKVIDGQENTWSNIYGQKYFEVQDGTTETNHGILDYLVVTSSK 246 G P M FAE Y GL+T ++D EN + K+FEV +ET H + ++V S K Sbjct: 186 GGTPTPMPFAEVYTGLKTGLVDAAENNLPSYEETKHFEVAPVYSETQHSMTPEVLVFSKK 245 Query: 247 WWDGLPADVRDQFAK-------ILNEVTIERNAESNKVEELNKQYIIEAGGVVRTLTPEQ 299 WD L ++ K ++ R A+++K + + G + T Sbjct: 246 VWDTLTPQEQEIIKKAAADSVPYYQKLWTAREADASKT-------VTKGGATIVASTQID 298 Query: 300 RQQWVDALKPVWQKFEK 316 R +V A++PVW K+EK Sbjct: 299 RAAFVKAMQPVWAKYEK 315 Lambda K H 0.316 0.132 0.383 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: 275 Number of extensions: 19 Number of successful extensions: 2 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: 332 Length of database: 330 Length adjustment: 28 Effective length of query: 304 Effective length of database: 302 Effective search space: 91808 Effective search space used: 91808 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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