GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-aldolase in Pseudomonas fluorescens FW300-N2E2

Align Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE; KDG aldolase YagE; Putative 2-dehydro-3-deoxy-D-pentonate aldolase YagE; EC 4.1.2.51; EC 4.1.2.28 (characterized)
to candidate Pf6N2E2_3203 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)

Query= SwissProt::P75682
         (302 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3203
          Length = 295

 Score =  128 bits (321), Expect = 2e-34
 Identities = 88/293 (30%), Positives = 146/293 (49%), Gaps = 8/293 (2%)

Query: 9   GIIPPVSTIFTADGQ-LDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARF 67
           GII    T F+ DGQ LD       ID LI +GV  +  LGS GE + L   E   ++ F
Sbjct: 8   GIIGYTITPFSTDGQGLDLDALGRSIDRLIDSGVHAIAPLGSTGEGAYLSDAEWDQVSEF 67

Query: 68  AIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQV 127
           +I  V  RVP ++        + +  ++ AQ  GAD ++V+   YWK+SEA ++ +++ +
Sbjct: 68  SIARVAGRVPTVVSVSDLTTAKAVHRARFAQAKGADVVMVLPASYWKLSEAEILAHYQAI 127

Query: 128 ADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAH 187
             S+ LP+MLYN PA +G D++  L+  + ++  N+  +K++   +  +  +    +G  
Sbjct: 128 GASIDLPIMLYNNPATSGIDMSVELILRIFNTVDNVTMVKESTGDIQRMHKLQLLGEGQV 187

Query: 188 PHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQ 247
           P +    G +         G  G  +A+ N  PQ++++L  A    D+++A        Q
Sbjct: 188 PFYN---GCNPLALEAFAAGAKGWCTAAPNLIPQLNLDLYAAVLANDLSQARALFYR--Q 242

Query: 248 IPQM-YQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQL 299
           +P + + L       IK  +   G  V    L P  PLDE R  QL+T+L+QL
Sbjct: 243 LPLLDFILKGGLPATIKAGLRTLGLEVGDPRL-PVFPLDEARNQQLQTMLKQL 294


Lambda     K      H
   0.320    0.138    0.407 

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: 209
Number of extensions: 11
Number of successful extensions: 1
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: 302
Length of database: 295
Length adjustment: 27
Effective length of query: 275
Effective length of database: 268
Effective search space:    73700
Effective search space used:    73700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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