GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fcbT3 in Burkholderia phytofirmans PsJN

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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