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 BPHYT_RS30450 BPHYT_RS30450 ABC transporter permease
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__BFirm:BPHYT_RS30450 Length = 619 Score = 173 bits (438), Expect = 2e-47 Identities = 137/434 (31%), Positives = 215/434 (49%), Gaps = 26/434 (5%) Query: 11 LGGTTVLLFL----------GLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASF 60 LG +L+F G+P+A+SF +L L ++ + +V ++ Sbjct: 194 LGNLNLLIFFVGLVALGVLSGVPIAFSFGLATF--GYLALTTNTPMPVVVGRMDEGMSHL 251 Query: 61 SLTPIPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIAT 120 L +PLF+ +G+L+ TG+A I + ++ + G L+ + V A S ISGS A Sbjct: 252 ILLSVPLFVFLGQLIEMTGMAAAMIAFLASLLGHVRGGLSYVLVGAMYLVSGISGSKAAD 311 Query: 121 TAMLGSLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGG 180 A + ++ P M ARG +P + + A G IPPS + + LGS+ G+SIS L GG Sbjct: 312 MAAVAPVLFPEMKARGAKPGDLVALLAATGAQTETIPPSLVLITLGSVTGVSISALFTGG 371 Query: 181 VLPGLLLAISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAV 240 +LPG++LAI+ IV + R E + RG E R+LV+ L+L FV AV Sbjct: 372 MLPGIVLAITLC--IVVQWRYRREDMSSVKRAT-RG-EILRKLVIAFPALALPFVIRAAV 427 Query: 241 ISGGVATPTEAAAIGCA-ATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFS 299 + G+AT TE + IG A A LA L+YR W+ L L T +SG IL II AAT + Sbjct: 428 VE-GIATATEVSTIGIAYAVLAGLLIYRRFEWKRLKPMLIDTATLSGAILLIIGAATAMA 486 Query: 300 QVLSFSGATNGIVDLVQSSGLPPAGVVAIMLA---ILIFLGLFVDQVSMMLLTLPFYMPI 356 L+ SG + L Q+ G P G M A + + LG ++ + ++L P PI Sbjct: 487 WALTQSGFSG---QLAQTLGALPGGAAMFMAASICMFVILGSVLEGIPAIVLFGPLMFPI 543 Query: 357 VKSLGIDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSF 416 +++ I + + ++ ++ M +GL PP G+ Y+ V+ H G + Y+ Sbjct: 544 ARAMHIHDVHYAMVVILSMGVGLFAPPFGVGYYSACAVSRIHPDEG--MKPILGYIAALM 601 Query: 417 TMLILIFFWPGIAT 430 LI++ P I+T Sbjct: 602 AGLIIVAAVPWIST 615 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: 634 Number of extensions: 32 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: 619 Length adjustment: 35 Effective length of query: 404 Effective length of database: 584 Effective search space: 235936 Effective search space used: 235936 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: 52 (24.6 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