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_RS20015 AZOBR_RS20015 C4-dicarboxylate ABC transporter
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__azobra:AZOBR_RS20015 Length = 503 Score = 214 bits (544), Expect = 7e-60 Identities = 132/438 (30%), Positives = 219/438 (50%), Gaps = 21/438 (4%) Query: 9 LLLGGTTVLLFLGLPVAYSFFA----INVVGAWLFLGGDSALGQLVRNGLVAVASFSLTP 64 L+ + L +G PVA++ A ++G L L + L + + +L Sbjct: 12 LMFAALVLFLLMGFPVAFALAANGLLFGLIGIELGLLTPALFQALPERVFGIMRNDTLLA 71 Query: 65 IPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAML 124 IP F MG +L +G+A+ +D + ++ L G LA + G +A +G A+ + Sbjct: 72 IPFFTFMGLILERSGMAEDLLDTVGQLFGPLRGGLAYAVIFVGALLAATTGVVAASVISM 131 Query: 125 GSLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPG 184 G + LP+ML GY+ +L G I A G + +IPPS + ++L G S+ + G ++PG Sbjct: 132 GLISLPIMLRYGYDRRLASGVIAASGTLAQIIPPSLVLIILADQLGRSVGDMYAGALVPG 191 Query: 185 LLLAISFVAYIVASAKLRPESAPR--EELVVLRGWE-RWRELVVYVLPLSLIFVAIVAVI 241 L+L + YI+ + +RPE P E LRG++ +R L V PL LIF+ ++ I Sbjct: 192 LVLTGLYAGYILVVSIVRPEFTPALPPEARSLRGFQLLFRVLTSLVPPLVLIFL-VLGTI 250 Query: 242 SGGVATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQV 301 G+ATPTE A+G A + + LM R L W + QA+ T +S ++FI++ +T F V Sbjct: 251 FIGIATPTEGGAMGAAGAMILALMKRQLSWSLMRQAMDTTAKLSSFVIFILIGSTVFGLV 310 Query: 302 LSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLG 361 + L+ S G + ++ ++ L F+D + + +P P+ + LG Sbjct: 311 FRAVNGDLWVEHLLTSLPGGELGFLIVVNIMVFLLAFFLDFFELAFIIVPLLAPVAEKLG 370 Query: 362 IDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAP-------------KHITMGQVFASA 408 ID IWFGV+ + MQ + PP G L+ ++ VAP K IT GQ++ A Sbjct: 371 IDLIWFGVLLGVNMQTSFMHPPFGFALFFLRSVAPREDYKDKITGKIIKKITTGQIYWGA 430 Query: 409 MPYVGLSFTMLILIFFWP 426 +P+V + M+ L+ +P Sbjct: 431 VPFVCIQLIMVALVIMFP 448 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: 586 Number of extensions: 45 Number of successful extensions: 5 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: 503 Length adjustment: 33 Effective length of query: 406 Effective length of database: 470 Effective search space: 190820 Effective search space used: 190820 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