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 WP_086510895.1 BZY95_RS16000 ABC transporter substrate-binding protein
Query= TCDB::Q9RBR1 (326 letters) >NCBI__GCF_002151265.1:WP_086510895.1 Length = 325 Score = 266 bits (679), Expect = 7e-76 Identities = 133/316 (42%), Positives = 193/316 (61%), Gaps = 1/316 (0%) Query: 9 SIAAAASVASAALPVRAQELVLRAVSAFPEKTSQSIHFEKFIERVNSTGKGVLRINYVGG 68 +I AA A + LR VS+F T+ FE F+E + + + IN++GG Sbjct: 10 TIGAALVSLGLVTQAAADTVTLRTVSSFNPGTAIPHTFEMFLEEIANDPDAPVEINFIGG 69 Query: 69 PRAIPTFEVGNAVKSGVVDIANCHGGYYANLFPEADALKLMQVTPQELRRSGGFDAINRI 128 P A+P F+VGNAV +GVVD+A +Y + P A AL L + +P+ELR +G F+ + + Sbjct: 70 PEAMPPFQVGNAVSNGVVDMAFVTSAFYTSSLPAAHALNLTRYSPEELRETGRFEQLQEM 129 Query: 129 WNAKGNMQYLAMIYGYSPFHLFLNKKISKPSELAGMKIRISPLYRDFLSALGVQVVNVAP 188 W + N+ YLA + +HL+LN+ I P +L G+++RI+P+YR F+ ALG + P Sbjct: 130 WREQMNVHYLAYTNYGNRYHLYLNEPIESP-DLNGLRLRITPVYRAFVEALGGEAAQTPP 188 Query: 189 GEIYTALERGVVEGYGWPIYSIFDLGWHEKTKYRVEPGFYNTETSIIMNLDSYKRLTSAQ 248 GE+YTALERG+V+GYGWP+ IFDLGW E T YRV+PGFY+ E +++N +++ LT Q Sbjct: 189 GEVYTALERGIVDGYGWPVQGIFDLGWQEHTSYRVDPGFYHVEVGVLVNQNTWDNLTDEQ 248 Query: 249 RAVLDPALAYAEGLNEDYKTINAREEKKQADAGIQVIRFEGEEGREFVRRAYDEGWKGII 308 R L + E LN + INA EE++QA+AGI+VI FEGE+ F+ AY+ W+ + Sbjct: 249 RDYLTEKAIWLEELNGLNEEINAEEERRQAEAGIEVIEFEGEDRERFLEMAYEVQWQRLA 308 Query: 309 ARAPENGPLLRRYLAS 324 EN LR L S Sbjct: 309 QEHAENTERLREILDS 324 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: 280 Number of extensions: 12 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: 325 Length adjustment: 28 Effective length of query: 298 Effective length of database: 297 Effective search space: 88506 Effective search space used: 88506 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 24 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