Align Citrate uptake transporter, substrate binding protein, component of Pmf-dependent citrate uptake porter, TctABC (characterized)
to candidate Pf1N1B4_4963 Tricarboxylate transport protein TctC
Query= TCDB::S5XTE7 (334 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4963 Length = 321 Score = 186 bits (472), Expect = 7e-52 Identities = 101/286 (35%), Positives = 161/286 (56%), Gaps = 4/286 (1%) Query: 53 IAPAAAGGGWDTFQREQQQSMRVNKIVNNIQVVNIPGAGGTIALGKLSTMTA--PNTLMV 110 +AP + GGG+D R ++M K + N GAGGT+ L + + T N L+V Sbjct: 34 MAPGSVGGGYDQTARVLGKAMVEAKTAKSTTFENKGGAGGTLGLAQFANGTKGDANALIV 93 Query: 111 GGTGHIAAQIQFDTPAKIQDVTPIARVVEEFDIITVPADSPYNTLEELIEGWKADPAGVS 170 G +AA Q ++DVTPIAR+ E+++I V DSPY TL +L++ +KA+P+ + Sbjct: 94 VGAIMVAAIEQNKPQITLKDVTPIARLFTEYNVIAVRDDSPYKTLGDLLKDFKANPSSIK 153 Query: 171 WTGG--GSFDQLVMTEIALSAGIDPKQTTFIPSDGGGEAIQALLNGTAKASTGGFADMYP 228 W GG GS D + + E+A + + ++ GGGE + A+L G TGG+A++ Sbjct: 154 WGGGSKGSIDHIGIAELASKMDVPVNKVNYVAFAGGGEVVAAVLGGHITVITGGYAELAK 213 Query: 229 QVEAGRLKVLGIAAEERLPGSDIPTLVEQGYDVTLTNWRAMFAPPGLSDDQIAELRAIVA 288 V++ + ++L I A R+ G D PTL E GYDVT+ NWR ++ GL+ +Q EL V Sbjct: 214 YVQSKQFRLLAIGAPNRVEGIDAPTLKEAGYDVTIGNWRGVYGAAGLTPEQRKELTEAVL 273 Query: 289 ESVETAEWQSAVERNYWMNASLEGEELDQFVEDEIDRIDQLFKEMG 334 + ++ WQ V+ N W + L G++ +FVE+E R+ + ++G Sbjct: 274 TATKSNVWQENVKTNAWSPSILTGDDFGKFVEEEHGRLRAMLVKVG 319 Lambda K H 0.314 0.131 0.375 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: 323 Number of extensions: 24 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: 334 Length of database: 321 Length adjustment: 28 Effective length of query: 306 Effective length of database: 293 Effective search space: 89658 Effective search space used: 89658 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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