GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsC in Escherichia coli BW25113

Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate 15742 b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)

Query= TCDB::Q8GBT6
         (403 letters)



>FitnessBrowser__Keio:15742
          Length = 530

 Score =  229 bits (585), Expect = 1e-64
 Identities = 145/424 (34%), Positives = 231/424 (54%), Gaps = 44/424 (10%)

Query: 5   QRIGRSLMLPVAVLPAAALLVRLGNA----------DMLGRPEFPAFVTKIAGFMAAGGN 54
           Q++G++ MLPVA+L    +++ +G++           +LG P   A  T    +M+  G+
Sbjct: 16  QQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVITLIPVLGNPVLQAIFT----WMSKIGS 71

Query: 55  AILDNMALLFAVGIAIGFAKKSDGSTALAAVVGYLVFKNVLATF--TDKNL-----PQVA 107
                + ++F + I +G A+++ G  A A  +GY V  N+   F  T+K +       V 
Sbjct: 72  FAFSFLPVMFCIAIPLGLARENKGVAAFAGFIGYAVM-NLAVNFWLTNKGILPTTDAAVL 130

Query: 108 KAVDGKVVMVDAPVDAKVLGGVVMGLVVALLYQRFYRTKLPDWAGFFGGRRLVPILSAFA 167
           KA + + ++    +D  +LG V+ G++V +L++RF+  +LPD   FFGG R VPI+S+  
Sbjct: 131 KANNIQSILGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIISSLV 190

Query: 168 GLVIGIVFGYIWPVLGTGLHNFGEWLVGSGAVGAGIFGVANRALIPIGMHHLLNSFPWF- 226
             ++G+V   +WP+   G+   G  +  +G  G  +FG   R L+P G+HH+L +   F 
Sbjct: 191 MGLVGLVIPLVWPIFAMGISGLGHMINSAGDFGPMLFGTGERLLLPFGLHHILVALIRFT 250

Query: 227 QAG---EYEGK--SGDIARFLAG---------DPTAGQFMT-GFFPIMMFALPAACLAIV 271
            AG   E  G+  SG +  F A            +A +F++ G  P  +  LP A LA+ 
Sbjct: 251 DAGGTQEVCGQTVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPGAALAMY 310

Query: 272 HCARPERRKVVGGMMFSLALTSFVTGVTEPIEFTFMFIAPVLYAIHAVLTGVSMALTWAL 331
           HCARPE R  + G++ S  +   V G TEP+EF F+F+APVLY IHA+LTG+   +   L
Sbjct: 311 HCARPENRHKIKGLLISGLIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGFTVMSVL 370

Query: 332 GMKDGFGFSAGAVDFFLNLGI---ASNPWGLA-LVGVCFAALYYVVFRFAITKFNLPTPG 387
           G+    G + G +  F+  GI    S  W +  +V   +  +YYV+FRFAIT+FNL TPG
Sbjct: 371 GVT--IGNTDGNIIDFVVFGILHGLSTKWYMVPVVAAIWFVVYYVIFRFAITRFNLKTPG 428

Query: 388 RESD 391
           R+S+
Sbjct: 429 RDSE 432


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: 672
Number of extensions: 37
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: 530
Length adjustment: 33
Effective length of query: 370
Effective length of database: 497
Effective search space:   183890
Effective search space used:   183890
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: 51 (24.3 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