Align Citrate uptake transporter, substrate binding protein, component of Pmf-dependent citrate uptake porter, TctABC (characterized)
to candidate Ac3H11_59 Tricarboxylate transport protein TctC
Query= TCDB::S5XTE7 (334 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_59 Length = 319 Score = 176 bits (446), Expect = 7e-49 Identities = 90/279 (32%), Positives = 151/279 (54%), Gaps = 4/279 (1%) Query: 48 SNMTLIAPAAAGGGWDTFQREQQQSMRVNKIVNNIQVVNIPGAGGTIALGKLSTMTA--P 105 S + ++ PA GGGWDT R ++M+ ++ N GA G I L + + Sbjct: 27 SAIKMMIPANPGGGWDTTGRALGKAMQDAGAAASVSYDNKGGAAGAIGLAQFVNASKGDA 86 Query: 106 NTLMVGGTGHIAAQIQFDTPAKIQDVTPIARVVEEFDIITVPADSPYNTLEELIEGWKAD 165 N +MV G + I P + VTP+AR+ E+++ +PA+SP+ T++++I+ K D Sbjct: 87 NAMMVMGAVMLGGIITGKPPVGLDKVTPLARLTSEYNVFVLPANSPFKTMKDVIDQLKKD 146 Query: 166 PAGVSWTGG--GSFDQLVMTEIALSAGIDPKQTTFIPSDGGGEAIQALLNGTAKASTGGF 223 P V W GG GS + + IA G+DP + ++ GGGEA A+L G G+ Sbjct: 147 PGSVKWGGGSRGSTEHIAAAMIAREVGVDPAKINYVAFRGGGEATAAILGGNVTVGGSGY 206 Query: 224 ADMYPQVEAGRLKVLGIAAEERLPGSDIPTLVEQGYDVTLTNWRAMFAPPGLSDDQIAEL 283 ++ + AG+++ +G+ + RL G ++PTL EQG +V + NWR ++ PG++ +Q L Sbjct: 207 SEFAEYITAGKMRPVGVTSGTRLKGVNVPTLKEQGINVEIGNWRGVYGAPGITPEQRKTL 266 Query: 284 RAIVAESVETAEWQSAVERNYWMNASLEGEELDQFVEDE 322 + ++ + WQ A+E+N W A + G+E FV+ E Sbjct: 267 IDALTKTYKHKAWQDAMEKNGWTPAWMAGDEFANFVDSE 305 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: 355 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: 334 Length of database: 319 Length adjustment: 28 Effective length of query: 306 Effective length of database: 291 Effective search space: 89046 Effective search space used: 89046 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