Align FcbT1, component of Tripartite 4-chlorobenzoate symporter (also binds and may transport 4-bromo-, 4-iodo-, and 4-fluorobenzoate and with a lower affinity, 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate) (characterized)
to candidate RR42_RS24120 RR42_RS24120 C4-dicarboxylate ABC transporter substrate-binding protein
Query= TCDB::Q9RBR1 (326 letters) >FitnessBrowser__Cup4G11:RR42_RS24120 Length = 327 Score = 289 bits (740), Expect = 6e-83 Identities = 150/315 (47%), Positives = 205/315 (65%), Gaps = 3/315 (0%) Query: 10 IAAAASVASAALPVRAQELVLRAVSAFPEKTSQSIHFEKFIERVNSTGKGVLRINYVGGP 69 +AA A + A+ A+E +R +AFPE TS K+ ERVNS GKG+++I+++GGP Sbjct: 8 LAATAVLGLLAVSAAAEEAQIRLATAFPENTSWVQELVKWSERVNSKGKGLVKISFIGGP 67 Query: 70 RAIPTFEVGNAVKSGVVDIANCHGGYYANLFPEADALKLMQVTPQELRRSGGFDAINRIW 129 RAIPTFE+GNAVKSGVVD+A G +Y N+FPEAD LK+ Q+ E R++G + IN++W Sbjct: 68 RAIPTFEIGNAVKSGVVDMALSPGAFYTNVFPEADMLKMAQIPVSEQRKNGAIEYINKVW 127 Query: 130 NAKGNMQYLA-MIYGYSPFHLFLNKKISKPSELAGMKIRISPLYRDFLSALGVQVVNVAP 188 N KGNM YLA M+ GY PFH+FL +KI K +L G KIR+SP R + AL V+N+ P Sbjct: 128 NEKGNMVYLARMVEGY-PFHIFLTQKIDK-LDLTGKKIRVSPAIRPAVQALNGNVINIPP 185 Query: 189 GEIYTALERGVVEGYGWPIYSIFDLGWHEKTKYRVEPGFYNTETSIIMNLDSYKRLTSAQ 248 GEIYTALER V++GYGW I IFDL TK+RV+PGFY+ + S+IMNLD +K +T Q Sbjct: 186 GEIYTALERSVIDGYGWSIGGIFDLKIAPLTKFRVDPGFYDADVSLIMNLDKWKSMTPQQ 245 Query: 249 RAVLDPALAYAEGLNEDYKTINAREEKKQADAGIQVIRFEGEEGREFVRRAYDEGWKGII 308 R + E + + E+KKQ +GIQ + F E +++ Y+ GW +I Sbjct: 246 RDFIQKMAMEIESNSSYWHKEGEDEKKKQNASGIQPLTFGAAETAKYLDAVYEAGWADLI 305 Query: 309 ARAPENGPLLRRYLA 323 +P +GP LR L+ Sbjct: 306 KTSPVHGPKLRALLS 320 Lambda K H 0.320 0.136 0.400 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: 302 Number of extensions: 6 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: 326 Length of database: 327 Length adjustment: 28 Effective length of query: 298 Effective length of database: 299 Effective search space: 89102 Effective search space used: 89102 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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