GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsC in Moritella dasanensis ArB 0140

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_017223048.1 A923_RS0117790 PTS glucose transporter subunit IIBC

Query= SwissProt::Q9S2H4
         (416 letters)



>NCBI__GCF_000276805.1:WP_017223048.1
          Length = 476

 Score =  306 bits (785), Expect = 7e-88
 Identities = 173/401 (43%), Positives = 246/401 (61%), Gaps = 21/401 (5%)

Query: 16  SGLFQGLQKVGRSLQLPIAVLPAAGIMVRLGQDDIFGKDGLGWDKVAAVFNNAGGALTGS 75
           S  F  LQKVG+SL LP++VLP AGI++ +G  +         + V+ +   AGG++ G 
Sbjct: 2   SNAFANLQKVGKSLMLPVSVLPVAGILLGIGAANFSFLP----EVVSQLMEQAGGSVFGQ 57

Query: 76  LPILFCIGVAIGFAKKADGSTALAAVVGFLVYSKVLEAFPVTEAVVQDGADVAATYNDPG 135
           + +LF +GVA+GF K  DG   L+A+VG+ + +  L    V   V+  G D      D G
Sbjct: 58  MALLFAVGVALGFTKN-DGVAGLSAIVGYGIMTATLS---VMAGVM--GVDKI----DTG 107

Query: 136 VLGGIIMGLLAAVLWQRYHRKKLVDWLGFFNGRRLVPIIMAFVGIVVGVFFGLVWEPIGD 195
           VLGGI+ G LA   + +++R +L ++LGFF G+R VPII  F  I +G    ++W PIG 
Sbjct: 108 VLGGILAGGLAGWAFNKFYRIQLPEYLGFFAGKRAVPIITGFCSIALGALLSVIWPPIGA 167

Query: 196 GISNFGEWMTGLGSGGA-ALFGGVNRALIPVGMHQFVNTVAWFQLGDFTNSAGDVVHGDI 254
            I+ F +W        A  ++G V RALIP G+H   N   +++ G  TN+AG + HG +
Sbjct: 168 VIATFSDWAAHQNPTVAFGIYGVVERALIPFGLHHIWNVPFFYEAGTCTNNAGGIAHGIM 227

Query: 255 TRFLAGDPSA-----GIFQ-AGFFPIMMFGLPAAALAMAHTARPERRKAVLGMMISLAAT 308
           T FL  D +      G  Q AG +   MFGLPAAA+A+AH+A+PE R  VLG+M S A T
Sbjct: 228 TCFLTADDATRAAGNGFGQLAGGYLFKMFGLPAAAIAIAHSAKPENRAKVLGIMASAALT 287

Query: 309 SFVTGVTEPIEFSFMFIAPVLYVLHAVLTAISMAITWGLGVHAGFNFSAGFIDYALNWHL 368
           SF+TG+TEPIEF+F+F+APVLYV+HA+L  ++  IT  +G+  G  FS GFID+ +    
Sbjct: 288 SFLTGITEPIEFAFLFVAPVLYVIHALLAGLAYVITNSMGIIHGHTFSNGFIDFVVQAPH 347

Query: 369 ATKPWLIIPIGLVFAAIYYVTFRFAIVKFNLKTPGREPEEE 409
           A K  L++ IG+ +AA+YY+ FR  I   +LKTPGRE E +
Sbjct: 348 AAKMPLLVGIGMAYAAVYYIVFRVVIKVLDLKTPGREDESD 388


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: 561
Number of extensions: 41
Number of successful extensions: 5
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: 476
Length adjustment: 32
Effective length of query: 384
Effective length of database: 444
Effective search space:   170496
Effective search space used:   170496
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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