GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsC in Burkholderia phytofirmans PsJN

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 BPHYT_RS02745 BPHYT_RS02745 PTS system N-acetylglucosamine-specific transporter subunit IIBC

Query= SwissProt::Q9S2H4
         (416 letters)



>FitnessBrowser__BFirm:BPHYT_RS02745
          Length = 591

 Score =  389 bits (998), Expect = e-112
 Identities = 200/396 (50%), Positives = 264/396 (66%), Gaps = 26/396 (6%)

Query: 19  FQGLQKVGRSLQLPIAVLPAAGIMVRLGQDDIFGKDGLGWDKVAAVFNNAGGALTGSLPI 78
           F  +Q++GR+L LPIAVLP AG+++RLGQ D+F            +  +AGGA+  +LP+
Sbjct: 6   FLKIQRLGRALMLPIAVLPVAGLLLRLGQPDVFN---------IKMIADAGGAIFDNLPL 56

Query: 79  LFCIGVAIGFAKKADGSTALAAVVGFLVYSKVLEAFPVTEAVVQDGADVAATYNDPGVLG 138
           LF IGVA+GFAK  +G   LA  +G+L+   V++             D+    N  GVL 
Sbjct: 57  LFAIGVAVGFAKDNNGVAGLAGAIGYLIEVAVMK-------------DINDKLN-MGVLS 102

Query: 139 GIIMGLLAAVLWQRYHRKKLVDWLGFFNGRRLVPIIMAFVGIVVGVFFGLVWEPIGDGIS 198
           GI+ G++A +L+ RY   KL D+L FF G+R VPI+   V +V+G+ FG VW+P+   I 
Sbjct: 103 GIVAGIVAGLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVID 162

Query: 199 NFGEWMTGLGSGGAALFGGVNRALIPVGMHQFVNTVAWFQLGDFTNSAGDVVHGDITRFL 258
             G W+T  G+ GA +FG +NR L+  G+H  +N++ WF  G FT   G  V GD+ RF 
Sbjct: 163 TAGHWLTTAGALGAFVFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFF 222

Query: 259 AGDPSAGIFQAGFFPIMMFGLPAAALAMAHTARPERRKAVLGMMISLAATSFVTGVTEPI 318
           AGDP+AG F  GFFP+MMFGLPAA LAM H A  ERR  V G++ S+A TSF+TGVTEPI
Sbjct: 223 AGDPTAGTFMTGFFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPI 282

Query: 319 EFSFMFIAPVLYVLHAVLTAISMAITWGLGVHAGFNFSAGFIDYALNWHLATKPWLIIPI 378
           EFSFMF+APVLYV+HA+LT IS+AI   LG+H GF FSAG IDY LN+ L+T+ W  IPI
Sbjct: 283 EFSFMFLAPVLYVIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPI 342

Query: 379 GLVFAAIYYVTFRFAIVKFNLKTPGREP---EEEVE 411
           GLV+  +YY  FRF I KFN+ TPGREP   +E+V+
Sbjct: 343 GLVYMVVYYGLFRFFIRKFNMATPGREPAAADEQVD 378


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: 740
Number of extensions: 39
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: 416
Length of database: 591
Length adjustment: 34
Effective length of query: 382
Effective length of database: 557
Effective search space:   212774
Effective search space used:   212774
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 (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