GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgA in Pseudomonas putida KT2440

Align 2-dehydro-3-deoxy-D-gluconate-6-phosphate aldolase (EC 4.1.2.55) (characterized)
to candidate PP_1024 PP_1024 KHG/KDPG aldolase

Query= metacyc::MONOMER-15645
         (213 letters)



>FitnessBrowser__Putida:PP_1024
          Length = 235

 Score =  207 bits (526), Expect = 2e-58
 Identities = 96/193 (49%), Positives = 143/193 (74%)

Query: 17  VVPVIVINKLEHAVPMAKALVAGGVRVLELTLRTECAVEAIRLIAQEVPDAIVGAGTVTN 76
           ++PVI I + E  +P+A AL AGG+R LE+TLR++  ++AI+++ ++ P+  VGAGTV +
Sbjct: 38  ILPVITIAREEDILPLADALAAGGIRTLEVTLRSQHGLKAIQVLREQRPELCVGAGTVLD 97

Query: 77  PQQLAEVTAAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYGLREFKFFP 136
               A V AAGAQF ++PG+T+ +L+A  +  IPL+PGIST SE+M+G   G R FK FP
Sbjct: 98  RSMFAAVEAAGAQFVVTPGITQDILEAGVDSEIPLLPGISTPSEIMMGYALGYRRFKLFP 157

Query: 137 AEANGGVKALQAIAGPFGKIRFCPTGGISLKNYRDYLALKSVLCVGGSWLVPADALESGD 196
           AE +GGV A++A  GPFG IRFCPTGG++  N R+Y+AL +V+CVGG+W++ +  +++GD
Sbjct: 158 AEISGGVAAIKAFGGPFGDIRFCPTGGVNPANVRNYMALPNVMCVGGTWMLDSSWIKNGD 217

Query: 197 YDRITALAREAVA 209
           + RI A + EA+A
Sbjct: 218 WARIEACSAEAMA 230


Lambda     K      H
   0.318    0.135    0.390 

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: 188
Number of extensions: 5
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: 213
Length of database: 235
Length adjustment: 22
Effective length of query: 191
Effective length of database: 213
Effective search space:    40683
Effective search space used:    40683
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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