GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Pseudomonas fluorescens FW300-N1B4

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Pf1N1B4_267 Enoyl-CoA hydratase (EC 4.2.1.17)

Query= metacyc::MONOMER-15953
         (257 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_267
          Length = 263

 Score =  117 bits (293), Expect = 2e-31
 Identities = 90/259 (34%), Positives = 125/259 (48%), Gaps = 29/259 (11%)

Query: 14  VRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKE---- 69
           V +I L R    NA +  LL+EL+      E D+E R  V+ G  + F AG D+      
Sbjct: 17  VLMIGLDRVAKRNAFDLNLLNELSLAYGEFEADSEARVAVVFGHGEHFTAGLDLVSAGAA 76

Query: 70  MAER--------DLVGILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIA 121
           +AE         D  G+L  PRV         SKP+I A  G+CL  G EL + ADI + 
Sbjct: 77  LAEGWQAPPGGCDPWGVLAGPRV---------SKPVIVAAQGYCLTVGIELMLAADINLC 127

Query: 122 GEDARFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTL 181
             + RF Q E+  GI P  G T RL +  G   AM+ +L+G   DA  A   GLV EV  
Sbjct: 128 ASNTRFAQKEVQRGIFPFGGATLRLHQVAGWGNAMRWLLTGDEFDAHDALHLGLVQEVMA 187

Query: 182 PELTIERALAIARVIAQKAPLAVRL----AKEALLKAEDTDLASGLRFERHAFTVLAGTA 237
            E  + RA+ +A  IA++APL V+     A++A  + E T   +     ++    L  + 
Sbjct: 188 SEDLLPRAIELAERIARQAPLGVQATLMSARQARYEGEMTAAQALPALVKN----LLNSE 243

Query: 238 DRAEGIRAFQEKRRPEFTG 256
           D  EG+R+  EKR   F G
Sbjct: 244 DAKEGVRSMIEKRPGVFKG 262


Lambda     K      H
   0.320    0.134    0.374 

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: 164
Number of extensions: 10
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: 257
Length of database: 263
Length adjustment: 24
Effective length of query: 233
Effective length of database: 239
Effective search space:    55687
Effective search space used:    55687
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: 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