GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_1946
          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:

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