GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ptsC in Pseudomonas fluorescens FW300-N2C3

Align PTS system N-acetylglucosamine-specific EIIC component; PTS system GlcNAc-specific EIIC component; GlcNAc-specific transporter; N-acetylglucosamine permease IIC component; GlcNAc permease IIC component (characterized)
to candidate AO356_17535 AO356_17535 PTS N-acetyl-D-glucosamine transporter

Query= SwissProt::Q9S2H4
         (416 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17535 AO356_17535 PTS
           N-acetyl-D-glucosamine transporter
          Length = 571

 Score =  374 bits (959), Expect = e-108
 Identities = 188/387 (48%), Positives = 261/387 (67%), Gaps = 24/387 (6%)

Query: 20  QGLQKVGRSLQLPIAVLPAAGIMVRLGQDDIFGKDGLGWDKVAAVFNNAGGALTGSLPIL 79
           +GLQ++GR+L LPIA+LP AG+++RLG  D+            A+ ++AG A+  +L ++
Sbjct: 7   EGLQRLGRALMLPIAILPIAGLLLRLGDTDLLD---------IAIIHDAGQAIFANLAMI 57

Query: 80  FCIGVAIGFAKKADGSTALAAVVGFLVYSKVLEAFPVTEAVVQDGADVAATYNDPGVLGG 139
           F IG+A+GFA+  +G+  LA  +G+LV    L+   V +A +           + G+L G
Sbjct: 58  FAIGIAVGFARDNNGTAGLAGAIGYLVMIATLK---VLDASI-----------NMGMLAG 103

Query: 140 IIMGLLAAVLWQRYHRKKLVDWLGFFNGRRLVPIIMAFVGIVVGVFFGLVWEPIGDGISN 199
           II GLLA  L+ R+   KL ++L FF GRR VPI+  F  + +GV FGL+W PI  GI+ 
Sbjct: 104 IISGLLAGALYNRFKDIKLPEYLAFFGGRRFVPIVTGFSAVGLGVVFGLIWPPIQQGING 163

Query: 200 FGEWMTGLGSGGAALFGGVNRALIPVGMHQFVNTVAWFQLGDFTNSA-GDVVHGDITRFL 258
           FG  +   GS GA +FG  NR LI  G+H  +N +AWF  G FT+ A G VV GD++R+ 
Sbjct: 164 FGALLMESGSFGAFVFGVFNRLLIVTGLHHILNNMAWFIFGSFTDPATGAVVTGDLSRYF 223

Query: 259 AGDPSAGIFQAGFFPIMMFGLPAAALAMAHTARPERRKAVLGMMISLAATSFVTGVTEPI 318
           AGDP  G F  G FP+M+FGLPAA LAM   A P+RRK + G+++S+A TSF+TGVTEPI
Sbjct: 224 AGDPKGGQFMTGMFPVMLFGLPAACLAMYRNALPQRRKVMGGILLSMALTSFLTGVTEPI 283

Query: 319 EFSFMFIAPVLYVLHAVLTAISMAITWGLGVHAGFNFSAGFIDYALNWHLATKPWLIIPI 378
           EF+FMF+AP+L+++HA+LT +SMA+T  LG+H GF FS GFID  L W  +T  WL++P+
Sbjct: 284 EFAFMFLAPLLFLVHALLTGVSMAVTNLLGIHLGFTFSGGFIDMVLGWGKSTNGWLVVPV 343

Query: 379 GLVFAAIYYVTFRFAIVKFNLKTPGRE 405
           GL +AAIYY+ F F I +F+LKTPGRE
Sbjct: 344 GLAYAAIYYLVFDFCIRRFDLKTPGRE 370


Lambda     K      H
   0.326    0.142    0.440 

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: 691
Number of extensions: 41
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: 416
Length of database: 571
Length adjustment: 34
Effective length of query: 382
Effective length of database: 537
Effective search space:   205134
Effective search space used:   205134
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 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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