GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Burkholderia phytofirmans PsJN

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate BPHYT_RS27190 BPHYT_RS27190 sugar ABC transporter permease

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>FitnessBrowser__BFirm:BPHYT_RS27190
          Length = 343

 Score =  212 bits (540), Expect = 1e-59
 Identities = 140/339 (41%), Positives = 187/339 (55%), Gaps = 28/339 (8%)

Query: 17  PAGTLGRLTTQER---LRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLA 73
           P   L R   Q R   ++    L  LV+L + FS+ +  F    NL  +A Q +    L 
Sbjct: 8   PNQALDRQVQQRRRDLIQKFAALGSLVVLIVAFSLTSAAFFSVGNLMTVALQVTSIAYLG 67

Query: 74  AGMTFVILTGGIDLSVGSILSISAVVAMLVSLMPQLGMLSVPAALLCGLLFGI----VNG 129
              T VI+TGGIDLSVGS+L+++ V A   +L+ + G+  +P A+L G+L G     VNG
Sbjct: 68  VAATCVIITGGIDLSVGSVLALAGVAA---ALLVKAGV-PIPVAMLGGMLVGAACGWVNG 123

Query: 130 ALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVL---------- 179
             V  M LPPFI TLG +   RGLA  +     +      F  +GNG +           
Sbjct: 124 ICVTRMGLPPFIATLGMMLVARGLALQITGARPVSGLGDAFGELGNGALFRISHIGADGF 183

Query: 180 ------GVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVY 233
                 G+P+ V+I   + A    +L RT LG  IYAVG NAEAARLSG+ V  V LF Y
Sbjct: 184 PDTVFPGIPYPVVIMVVLFAAVSILLSRTSLGRHIYAVGSNAEAARLSGVNVQGVKLFTY 243

Query: 234 AVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGAL 293
            +SGLLAG  G +  +RL  A   + G  YELDAIA+ ++GGTS +GG G+I GT +GA 
Sbjct: 244 VLSGLLAGATGCVLMSRLVTAQPNE-GVMYELDAIASAVIGGTSLMGGVGTISGTAIGAF 302

Query: 294 IIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSYRRK 332
           +I VL NGL + GVS   Q II G+VI+G V +D  R +
Sbjct: 303 VIGVLRNGLNMNGVSSFIQQIIIGVVILGTVWIDQLRNR 341


Lambda     K      H
   0.325    0.141    0.409 

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: 399
Number of extensions: 23
Number of successful extensions: 4
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: 337
Length of database: 343
Length adjustment: 28
Effective length of query: 309
Effective length of database: 315
Effective search space:    97335
Effective search space used:    97335
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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