GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsC in Amycolatopsis xylanica CPCC 202699

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 WP_091292425.1 BLV57_RS24320 PTS transporter subunit EIIC

Query= SwissProt::Q9S2H4
         (416 letters)



>NCBI__GCF_900107045.1:WP_091292425.1
          Length = 409

 Score =  395 bits (1015), Expect = e-114
 Identities = 210/417 (50%), Positives = 278/417 (66%), Gaps = 17/417 (4%)

Query: 3   TATDTAAPAKKRGSGLFQGLQKVGRSLQLPIAVLPAAGIMVRLGQDDIFGKDGLGWDKVA 62
           +AT  A   + RG     GLQ+ GRSL LPIA LPAAGI++RLGQ+D+ G  GLGWDKVA
Sbjct: 2   SATTAAGKGQSRG---LAGLQRFGRSLMLPIAALPAAGILLRLGQEDLLGPKGLGWDKVA 58

Query: 63  AVFNNAGGALTGSLPILFCIGVAIGFAKKADGSTALAAVVGFLVYSKVLEAFPVTEAV-- 120
            VF  AGG L   LP+LF + +A+GFA+K DGSTA+AAVVG++V++ V++ F   ++V  
Sbjct: 59  DVFAAAGGGLFDWLPLLFAVAIAVGFARKGDGSTAVAAVVGWIVFNHVVQVFAPIKSVEG 118

Query: 121 VQDGADVAATYNDPGVLGGIIMGLLAAVLWQRYHRKKLVDWLGFFNGRRLVPIIMAFVGI 180
            ++G  +A       VLGG+++GL+AA+LWQ+YHR KL  +L FF GRR VPII +FV I
Sbjct: 119 FKEGWYLAPIKWPYSVLGGVVVGLVAALLWQKYHRIKLPAYLAFFGGRRFVPIITSFVMI 178

Query: 181 VVGVFFGLVWEPIGDGISNFGEWMTGLGSGGAALFGGVNRALIPVGMHQFVNTVAWFQLG 240
           ++GV FGL+++ +   I   GE  T     G  ++G +NR LIP+G+HQ +N   WF   
Sbjct: 179 ILGVLFGLIFKQVDHVIHWVGEQATANSVVGGGVYGLLNRLLIPIGLHQLLNVPVWFIFD 238

Query: 241 DFTNSAGDVVHGDITRFLAGDPSAGIFQAGFFPIMMFGLPAAALAMAHTARPERRKAVLG 300
                      GD+  F      +G F  GFFPI MF LPAAALA+  TA+P ++K V G
Sbjct: 239 G----------GDLNNFFNHVQGSGSFMTGFFPIFMFALPAAALAIWQTAKPSQKKVVGG 288

Query: 301 MMISLAATSFVTGVTEPIEFSFMFIAPVLYVLHAVLTAISMAITWGLGVHAGFNFSAGFI 360
           +MI+ A TSF+TGVTEPIEF+FMF+A  LY+ HAV+T +SM +   LG+  GF+FSAG I
Sbjct: 289 VMIAAALTSFLTGVTEPIEFAFMFVAWPLYLFHAVMTGLSMVLVNALGIKLGFSFSAGAI 348

Query: 361 DYALNWHL--ATKPWLIIPIGLVFAAIYYVTFRFAIVKFNLKTPGREPEEEVEDLTK 415
           D+A N  L  A K W++IPIGLVFA IY+  F+F I K+NL TPGRE +    DL K
Sbjct: 349 DFAFNSSLDTANKAWMLIPIGLVFAVIYFFVFKFVITKWNLATPGREDDSIEADLEK 405


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: 640
Number of extensions: 46
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: 409
Length adjustment: 31
Effective length of query: 385
Effective length of database: 378
Effective search space:   145530
Effective search space used:   145530
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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