GapMind for catabolism of small carbon sources

 

Aligments for a candidate for LRA5 in Pseudomonas putida KT2440

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate PP_1946 PP_1946 Oxidoreductase, short chain dehydrogenase/reductase family

Query= SwissProt::Q1NEI6
         (249 letters)



>lcl|FitnessBrowser__Putida:PP_1946 PP_1946 Oxidoreductase, short
           chain dehydrogenase/reductase family
          Length = 262

 Score =  142 bits (359), Expect = 5e-39
 Identities = 80/242 (33%), Positives = 126/242 (52%), Gaps = 4/242 (1%)

Query: 8   YAGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGD----ALAATQAEIDATHVVALD 63
           ++G+  +VTG  SG+G+  A      G +VA+ D++ D     +   +AE        +D
Sbjct: 7   FSGKVVLVTGAGSGIGRATALAFAQSGASVAVADISTDHGLKTVELVKAEGGEATFFHVD 66

Query: 64  VSDHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCN 123
           V    +V +      A  G +DI   +AGI    VP+ E   D+++RVID+NL+ +FYC 
Sbjct: 67  VGSEPSVQSMLAGVVAHYGGLDIAHNNAGIEANIVPLAELDSDNWRRVIDVNLSSVFYCL 126

Query: 124 REVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANA 183
           +  +P ML+ G G IVN AS +G  G    S Y+A+K GV+G TK+   + A + +  NA
Sbjct: 127 KGEIPLMLKRGGGAIVNTASASGLIGGYRLSGYTATKHGVVGLTKAAAIDYANQNIRINA 186

Query: 184 LTPATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTS 243
           + P   +SP L  +PQ   D +    P+GRL   EE A  V ++ S++  +    +    
Sbjct: 187 VCPGPVDSPFLADMPQPMRDRLLFGTPIGRLATAEEIARSVLWLCSDDAKYVVGHSMSVD 246

Query: 244 GG 245
           GG
Sbjct: 247 GG 248


Lambda     K      H
   0.318    0.132    0.381 

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: 179
Number of extensions: 9
Number of successful extensions: 2
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: 249
Length of database: 262
Length adjustment: 24
Effective length of query: 225
Effective length of database: 238
Effective search space:    53550
Effective search space used:    53550
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: 47 (22.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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