Align Tricarboxylate transport protein TctC (characterized)
to candidate RR42_RS20620 RR42_RS20620 C4-dicarboxylate ABC transporter substrate-binding protein
Query= reanno::Dino:3609740 (326 letters) >FitnessBrowser__Cup4G11:RR42_RS20620 Length = 310 Score = 189 bits (480), Expect = 8e-53 Identities = 101/310 (32%), Positives = 166/310 (53%), Gaps = 4/310 (1%) Query: 15 AALAMTGGAHAEGEQMLESIHFLIPGGAGGGWDGTARGTGEALTKAGLVGSASYENMSGG 74 A+ A+T A L+S+ F+I GGG+D T R G AL AG+ +ASY+N G Sbjct: 2 ASAAITATVAAAPAFALDSVKFMIGANPGGGFDQTGRSLGAALVSAGVAKTASYDNKGGA 61 Query: 75 GGGKAIAYLIENANSSHGTLMVNSTPIVIRSLTGEISQSFRDLTLVAGTIGDYAAIVVGK 134 GG + + + ++V +V T + ++ T +A D I V Sbjct: 62 GGTIGLTQFVNTDKGNPNAMIVTGAVMVGAIETNHPPVTLKNATPIARLFADTMVITVPA 121 Query: 135 DSPINSMADLIAAYDADPNATAVGGGSVPGGMDHLVAAMVMEAAGKDALGVKYIPYDAGG 194 +SP+ SM DL A A+P + + GGGS G +DH++A +V + +G D + Y+P+ GG Sbjct: 122 NSPLKSMKDLTAQLRANPGSVSWGGGS-KGSIDHILAGLVAKESGVDPKKINYVPFQGGG 180 Query: 195 KAMAALLSGEIAALSTGFSEAIDLAEAGEVKIIGVTAPERVAAYDSAPTMVEQGIDTTFV 254 +A A++L G + G SE + ++G+++ + VT+ +R A PT+ EQGI+ Sbjct: 181 EASASILGGHVTVGLAGVSEFLPFIKSGKMRALAVTSKDRTA---DIPTLKEQGINVEIY 237 Query: 255 NWRGFFAAPGLPEEQLAAYQATLEKMYDTPEWEEVRARNGWVNIHNSGADFQSFLEAQEA 314 NWRG + APG+ EQ A + K +TP W+E A+N W +G +F F++++ A Sbjct: 238 NWRGVYGAPGITAEQRKALVDAVVKATETPLWKETLAKNDWTPFLLTGDEFGKFVDSESA 297 Query: 315 QIGDLMKKLG 324 ++G +++LG Sbjct: 298 RLGGSLRELG 307 Lambda K H 0.315 0.132 0.378 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: 287 Number of extensions: 19 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: 326 Length of database: 310 Length adjustment: 27 Effective length of query: 299 Effective length of database: 283 Effective search space: 84617 Effective search space used: 84617 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: 42 (22.0 bits) S2: 48 (23.1 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