Align FcbT3, 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 AZOBR_RS14700 AZOBR_RS14700 C4-dicarboxylate ABC transporter permease
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__azobra:AZOBR_RS14700 Length = 433 Score = 236 bits (601), Expect = 1e-66 Identities = 134/427 (31%), Positives = 238/427 (55%), Gaps = 9/427 (2%) Query: 15 TVLLFLG--LPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASFSLTPIPLFILMG 72 T+LL LG + VA + + V LF + + N A S++LT +PLFI MG Sbjct: 13 TMLLMLGTGIWVALALAGVGFVAMALFTTRPVGM-VMATNIWGASTSWTLTALPLFIWMG 71 Query: 73 ELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGSLMLPMM 132 E+LF T ++ G+ LPGRL + +V T F+A+SGS+ AT A +G + +P + Sbjct: 72 EILFRTRISSDMFKGLAPWTGWLPGRLMHVNIVGCTIFAAVSGSSAATAATIGRMTIPEL 131 Query: 133 LARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGLLLAISFV 192 RGY+P + +G + G + +LIPPS + ++ G A +SI++L I GV+PG++L F+ Sbjct: 132 TRRGYDPMMIVGSLAGAGTLGLLIPPSIIMIVYGVAADVSIARLFIAGVIPGIVLTGLFM 191 Query: 193 AYIVASAKLRPESA-PREELVVLRGWERWRELVVYVLPLSLIFVAIVAVISGGVATPTEA 251 Y+ + L P+ PRE L E+ R+ ++P+ L+ ++ I G+ATPTEA Sbjct: 192 LYVGGWSLLNPDRVPPREARQSL--MEKIRD-TGSLIPVMLLIAGVLGSIYAGIATPTEA 248 Query: 252 AAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLSFSGATNGI 311 A IG +L + L+ + W + ++ G S MI FI+ A + + ++G + Sbjct: 249 AGIGVLGSLLLALVTGTMSWATFRDSVMGAAHTSCMIGFILAGAAFLTVAMGYTGIPRLL 308 Query: 312 VDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGIDQIWFGVMY 371 + + S L A ++ ++ I +G F+D +SM++LT +P+V++ GID +WFG+ Sbjct: 309 AEWITSMQLTTASLLVVLTLFFIVMGCFLDGISMVVLTTSVILPMVQNAGIDLLWFGIYI 368 Query: 372 LICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIFFWPGIATW 431 +I +++ + PP G L+ ++ + K+I + +++P+ + M+ L++ +PG+ +W Sbjct: 369 IIVVEMAQITPPVGFNLFVLQSMTGKNIF--TIAKASLPFFLMMIVMVALLWIFPGMVSW 426 Query: 432 LPDVFVG 438 LP + +G Sbjct: 427 LPSLMIG 433 Lambda K H 0.329 0.143 0.433 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: 489 Number of extensions: 25 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: 439 Length of database: 433 Length adjustment: 32 Effective length of query: 407 Effective length of database: 401 Effective search space: 163207 Effective search space used: 163207 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 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