GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Dyella japonica UNC79MFTsu3.2

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate N515DRAFT_0416 N515DRAFT_0416 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase

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



>FitnessBrowser__Dyella79:N515DRAFT_0416
          Length = 686

 Score =  102 bits (253), Expect = 3e-26
 Identities = 69/192 (35%), Positives = 103/192 (53%), Gaps = 10/192 (5%)

Query: 11  EQGVRLITLQRPEA-LNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKE 69
           + G+  +TL R  + +NAL+ ++LDEL   +     +     ++ +     FA GADIKE
Sbjct: 16  DSGIVTLTLDRANSSVNALSREVLDELGQIVERLSIEKPAGVLIHSAKPGGFAVGADIKE 75

Query: 70  MAE--RD---LVGILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGED 124
             E  RD   L  I    RV  ++ +A    P +AA++G C+GGG EL +     IA +D
Sbjct: 76  FVEYARDGTVLQNIENGQRV--FESLARLPCPTVAAIHGACMGGGTELVLACRQRIAADD 133

Query: 125 --ARFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLP 182
              R G PE+ LGI PG GGT RL R +G   A+ ++L+G+A+ AR A   G+V  +  P
Sbjct: 134 EKTRIGLPEVMLGIHPGWGGTARLPRLIGALDALPVMLTGKALSARRAAALGVVDRLAPP 193

Query: 183 ELTIERALAIAR 194
              +  A A+ R
Sbjct: 194 NELLAEARALLR 205


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: 421
Number of extensions: 17
Number of successful extensions: 3
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: 686
Length adjustment: 31
Effective length of query: 226
Effective length of database: 655
Effective search space:   148030
Effective search space used:   148030
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: 50 (23.9 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