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 WP_086510893.1 BZY95_RS15990 TRAP transporter large permease
Query= TCDB::Q9RBQ9 (439 letters) >NCBI__GCF_002151265.1:WP_086510893.1 Length = 438 Score = 459 bits (1182), Expect = e-134 Identities = 229/436 (52%), Positives = 315/436 (72%), Gaps = 1/436 (0%) Query: 1 MNWQLAAWLLLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASF 60 M W A LL+GG +L+ LGLPV ++F AIN+VGA++F+GG+ + Q+ RN A+ SF Sbjct: 1 MEWHSALLLLVGGLILLMALGLPVVFAFIAINLVGAYVFMGGEMGIMQMARNSAEAITSF 60 Query: 61 SLTPIPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIAT 120 SL PIPLF+LMGE+LFHTGLA +AI I+++I +PGRL++++V+ GT F+ +SGS+IA Sbjct: 61 SLIPIPLFVLMGEVLFHTGLAYKAITAIERLIKGVPGRLSIVSVLGGTAFATLSGSSIAN 120 Query: 121 TAMLGSLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGG 180 TAM+GS +LP ML RGY P + MGPI+A+GG+ MLIPPSALAV LGSLAGISI +LLIGG Sbjct: 121 TAMMGSSLLPDMLKRGYHPSIAMGPIMAVGGIAMLIPPSALAVTLGSLAGISIGQLLIGG 180 Query: 181 VLPGLLLAISFVAYIVASAKLRPESAPREE-LVVLRGWERWRELVVYVLPLSLIFVAIVA 239 ++PG+L+ IS + Y++ PE AP +E L WERW+ VYVLPLS IFVA+V Sbjct: 181 IIPGILMGISVLLYVMIRCARNPELAPADEGNPSLTTWERWQPFCVYVLPLSGIFVAVVG 240 Query: 240 VISGGVATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFS 299 + G A PTE+AA G A + YR L Q+LV AL T +S MILF++VA+TTFS Sbjct: 241 SLLAGWAEPTESAAFGAVAATVAAMCYRCLTRQALVTALMETAKVSVMILFVLVASTTFS 300 Query: 300 QVLSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKS 359 Q+LSFSGAT G++ ++ + L P +V ML +L+ LG F DQ+SM+++TLPF+MP+V S Sbjct: 301 QLLSFSGATRGLLQVITAWDLTPLMIVLGMLLVLLVLGCFADQISMIMITLPFFMPLVSS 360 Query: 360 LGIDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTML 419 LGID IW GV++L+ M++ L PP G+LL M+GVAP I + QV+ +A+P++ L +L Sbjct: 361 LGIDPIWIGVLFLVAMEISFLTPPFGLLLIVMQGVAPPGIRLTQVYQAALPFLLLQLLVL 420 Query: 420 ILIFFWPGIATWLPDV 435 L+ P +AT LP++ Sbjct: 421 ALVVAVPWLATGLPNL 436 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: 526 Number of extensions: 21 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: 439 Length of database: 438 Length adjustment: 32 Effective length of query: 407 Effective length of database: 406 Effective search space: 165242 Effective search space used: 165242 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 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