GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsC in Caulobacter crescentus NA1000

Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate CCNA_00572 CCNA_00572 PTS system, N-acetylglucosamine-specific IIBC component

Query= TCDB::Q8GBT6
         (403 letters)



>FitnessBrowser__Caulo:CCNA_00572
          Length = 582

 Score =  384 bits (985), Expect = e-111
 Identities = 197/401 (49%), Positives = 267/401 (66%), Gaps = 10/401 (2%)

Query: 1   MAVLQRIGRSLMLPVAVLPAAALLVRLGNADMLGRPEFPAFV----TKIAGFMAAGGNAI 56
           + +LQ +GR+LMLP+AVLP AALL+R+G  D+LG P   A        +A    A G AI
Sbjct: 5   LEILQPLGRALMLPIAVLPVAALLLRIGQPDLLGAPALAAATHGMSLSVANTFGAAGGAI 64

Query: 57  LDNMALLFAVGIAIGFAKKSDGSTALAAVVGYLVFKNVLATFTDKNLPQVAKAVDGKVVM 116
             ++ L+FA+G+A+G A+++ G+  LA VV Y++    +           AKAV+G   +
Sbjct: 65  FASLGLIFAIGVAVGLARENHGAAGLAGVVCYVIATKGVEALLVAPPEVAAKAVEGAKDL 124

Query: 117 VDAPVDAKVLG------GVVMGLVVALLYQRFYRTKLPDWAGFFGGRRLVPILSAFAGLV 170
             A   AK +G      G++ G++   LY R+   +LP++  FFGGRR VPI++  AG+V
Sbjct: 125 AIAAWKAKEIGKLSIPVGILSGVISGALYNRYSTIQLPEYLAFFGGRRFVPIVAGLAGVV 184

Query: 171 IGIVFGYIWPVLGTGLHNFGEWLVGSGAVGAGIFGVANRALIPIGMHHLLNSFPWFQAGE 230
           + ++FG  W  L  G+      +  SG +G  ++G+ NR LI  G+HH+LN+  WF  G+
Sbjct: 185 LALLFGAFWSTLEAGVDGLSGLVTASGDLGLVVYGLLNRLLIVTGLHHILNNVVWFILGD 244

Query: 231 YEGKSGDIARFLAGDPTAGQFMTGFFPIMMFALPAACLAIVHCARPERRKVVGGMMFSLA 290
           + G +GD+ RF AGD TAG FM+GFFP+MMF LPAACLA++H ARPERRK V GM+ SLA
Sbjct: 245 FNGVTGDLNRFAAGDKTAGAFMSGFFPVMMFGLPAACLAMLHTARPERRKAVAGMLGSLA 304

Query: 291 LTSFVTGVTEPIEFTFMFIAPVLYAIHAVLTGVSMALTWALGMKDGFGFSAGAVDFFLNL 350
           LTSF+TGVTEPIEFTFMF+APVL+AIHA+LTG+SMAL   L +K GFGFSAG  D+ LN 
Sbjct: 305 LTSFLTGVTEPIEFTFMFLAPVLFAIHALLTGLSMALMNMLDVKLGFGFSAGLFDYVLNF 364

Query: 351 GIASNPWGLALVGVCFAALYYVVFRFAITKFNLPTPGRESD 391
             A+ P  L  VG+ + ALYY VFRFAI +F+L TPGRE +
Sbjct: 365 NKATRPLLLIPVGLVYGALYYGVFRFAILRFDLKTPGREDE 405


Lambda     K      H
   0.328    0.143    0.441 

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: 726
Number of extensions: 44
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: 403
Length of database: 582
Length adjustment: 34
Effective length of query: 369
Effective length of database: 548
Effective search space:   202212
Effective search space used:   202212
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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