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 GFF360 Psest_0361 TRAP transporter, DctM subunit
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__psRCH2:GFF360 Length = 426 Score = 197 bits (501), Expect = 5e-55 Identities = 130/432 (30%), Positives = 225/432 (52%), Gaps = 13/432 (3%) Query: 7 AWLLLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASFSLTPIP 66 A +LLG VL+ L +PVAYS +VGAW D L ++ V FSL IP Sbjct: 3 AVVLLGSFIVLILLRVPVAYSLGLATLVGAWWI---DIPLHAVMIQIAGGVNKFSLLAIP 59 Query: 67 LFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGS 126 F+L G ++ G+A+R + ++ + G L+++ + A TFF AISGS++A TA +GS Sbjct: 60 FFVLAGAIMAEGGMARRLVAFAGVLVGFVRGGLSLVNITASTFFGAISGSSLADTASVGS 119 Query: 127 LMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAG--ISISKLLIGGVLPG 184 +++P M +GY + I+ +L PPS +V+ AG +SI+ L + G+ PG Sbjct: 120 VLIPEMEKKGYPREFSTAVTISGSVQALLTPPSHNSVIYSLAAGGTVSIAALFVAGIGPG 179 Query: 185 LLLAISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAVISGG 244 LLL+ + + A+ R + P+ E+V LR + ++ V L + V I+ I G Sbjct: 180 LLLSATMATLCLLFARKR--NYPKGEVVPLR---QALKICVEALWGLMTMVIILGGILSG 234 Query: 245 VATPTEAAAIGCAATLAITL-MYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLS 303 V T TE+AA+ +T+ +YR +W L + L TV +++ +I A +F +++ Sbjct: 235 VFTATESAAVAVVWAFFVTMFIYRDYKWSELPRMLHRTVRTLSIVMILIAFAASFGYIMT 294 Query: 304 FSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGID 363 + I + ++ + +L+ LG +D ++L+ P +P+V S G+D Sbjct: 295 LMQIPSKITTAFLALSDNRYVILMCINFMLLVLGTLMDMAPLILILTPILLPVVVSFGVD 354 Query: 364 QIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIF 423 + FG++ L+ + +GL+ PP G +L+ G A +T+ + +P+ F +L+ + Sbjct: 355 PVHFGMIMLVNLGIGLITPPVGAVLFV--GAAIGKVTIENTVKALLPFYAALFAVLMAVT 412 Query: 424 FWPGIATWLPDV 435 + P I+ WLP V Sbjct: 413 YIPMISLWLPSV 424 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: 437 Number of extensions: 23 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: 426 Length adjustment: 32 Effective length of query: 407 Effective length of database: 394 Effective search space: 160358 Effective search space used: 160358 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