GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Burkholderia phytofirmans PsJN

Align GtsC (GLcG), component of Glucose porter, GtsABCD (characterized)
to candidate BPHYT_RS22780 BPHYT_RS22780 sugar ABC transporter permease

Query= TCDB::Q88P36
         (281 letters)



>FitnessBrowser__BFirm:BPHYT_RS22780
          Length = 283

 Score =  189 bits (479), Expect = 8e-53
 Identities = 103/282 (36%), Positives = 167/282 (59%), Gaps = 7/282 (2%)

Query: 4   PVDKPVLSLSRMAIHAVLLIAVLLYLVPLVVMLLTSFKTPEDITTGNLLSWP---AVITG 60
           P+DK   +  RM     L +A+L++L+P++ +L+TS ++ E+++ GN   WP   A+   
Sbjct: 5   PIDKWKPATRRM-YKLTLPVALLIWLLPMIAVLVTSVRSTEELSEGNYWGWPKHFAMFDN 63

Query: 61  IGWVKAWGAVSGYFWNSIMITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFL 120
                    +  YFWNS++ITVPAV+ S A+ A+ G+ L+++RFRG+   F   + G F+
Sbjct: 64  YREALTTSPMLHYFWNSVLITVPAVVGSIALAAMAGFALAIYRFRGNSTLFATFVAGNFV 123

Query: 121 PFQTVLLPASFTLGKLGLASTTGGLVLVHVVYGLAFTTLFFRNFYVSIPDALVKAARLDG 180
           P Q +++P      +LGL +T   L+L HV +   F  LF RNF   +P  LV+AAR++G
Sbjct: 124 PVQVLMIPVRDLSLQLGLFNTVSALILFHVSFQTGFCALFLRNFIKQLPFELVEAARIEG 183

Query: 181 AGFFTIFRRIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSG-DSQPITVALNNLVNTS 239
           A  +T+F +I+LP+  P +    I  FT +WND+ + +  + G D+ PITV +  L    
Sbjct: 184 ANEWTVFFKIVLPLIRPALAALAILVFTFVWNDYFWALCLTQGDDAAPITVGVAALKGQW 243

Query: 240 TGAKEYNVDMAAAMIAGLPTLLVYVVAGKYFVRGLTAGAVKG 281
           T A  +N+  A +++A LP++ ++    K+FV GLT GA KG
Sbjct: 244 TTA--WNLVSAGSILAALPSVAMFFAMQKHFVAGLTFGATKG 283


Lambda     K      H
   0.329    0.142    0.443 

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: 212
Number of extensions: 11
Number of successful extensions: 3
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: 281
Length of database: 283
Length adjustment: 26
Effective length of query: 255
Effective length of database: 257
Effective search space:    65535
Effective search space used:    65535
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: 47 (22.7 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