GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Burkholderia phytofirmans PsJN

Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate BPHYT_RS05035 BPHYT_RS05035 sugar ABC transporter permease

Query= reanno::WCS417:GFF4322
         (281 letters)



>FitnessBrowser__BFirm:BPHYT_RS05035
          Length = 285

 Score =  369 bits (946), Expect = e-107
 Identities = 183/284 (64%), Positives = 224/284 (78%), Gaps = 9/284 (3%)

Query: 7   KPAISLSRIAIYAVLILAVLLYLVPLVVMLLTSFKTPEDISSGNLLSWPTVVTGIGWVKA 66
           +P +++SR  IYA L L  L +L PL VML TSFK  + + +GNLL+ PT  T   W+KA
Sbjct: 2   QPKMTISRAVIYAALFLFALYFLFPLYVMLSTSFKDIDQLRTGNLLTPPTHWTIDPWIKA 61

Query: 67  WATV------DG---YFWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFG 117
           W+        DG   +F NS+++ +PAVLIS+ IGA NGYVL+ WRF+G+   F ++L G
Sbjct: 62  WSGACTGVRCDGMQPFFMNSVRMVIPAVLISSIIGAFNGYVLTHWRFRGADPIFTMILVG 121

Query: 118 CFLPFQTVLLPASFTLGKMGLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAAR 177
           CF+PFQ +LLP +   G +GL++TTTGLV VHV+YG+AFTT+FFRN+YVSIP  L+KAAR
Sbjct: 122 CFIPFQAILLPMARFEGFLGLSNTTTGLVVVHVIYGIAFTTMFFRNFYVSIPAELVKAAR 181

Query: 178 LDGAGFFTIFRQIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVN 237
           +DGAGFFTIF +I+LP+S PI MVCLIWQFTQIWNDFLFG+VFS  DS PITVALNNLVN
Sbjct: 182 IDGAGFFTIFTKILLPVSLPIFMVCLIWQFTQIWNDFLFGIVFSGVDSMPITVALNNLVN 241

Query: 238 TSTGAKEYNVDMAAAMIAGLPTLLVYVIAGKYFVRGLTAGAVKG 281
           TSTG KEYNVDMA A+IA LPTLLVY+IAG+YFVRGLTAGAVKG
Sbjct: 242 TSTGVKEYNVDMAGAIIAALPTLLVYIIAGRYFVRGLTAGAVKG 285


Lambda     K      H
   0.328    0.141    0.435 

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: 303
Number of extensions: 7
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: 281
Length of database: 285
Length adjustment: 26
Effective length of query: 255
Effective length of database: 259
Effective search space:    66045
Effective search space used:    66045
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