GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Dokdonella koreensis DS-123

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_067646635.1 I596_RS08905 enoyl-CoA hydratase

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>NCBI__GCF_001632775.1:WP_067646635.1
          Length = 264

 Score =  111 bits (277), Expect = 2e-29
 Identities = 83/260 (31%), Positives = 123/260 (47%), Gaps = 8/260 (3%)

Query: 6   ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGA 65
           I ++ RG    + L+RP   NA + AL+ EL AAL+  DAD A+ A+VVTG+   F+AGA
Sbjct: 5   IQIDRRGSAAYLVLDRPGVHNAFDAALIAELTAALKSLDADPAVRAVVVTGAGATFSAGA 64

Query: 66  DIGMMSTYTYMDVYKGD----YITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIF 121
           D+  M +    D  +       + +   T+  + KP IA V G A GGG  L   CDI  
Sbjct: 65  DLNWMRSMAAADEAENRADSLRLAQLMRTLNFLSKPTIARVNGSAYGGGVGLVACCDIAV 124

Query: 122 AADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVI 181
             ++AKF   E KLG++P A  +  +  A+   +A     +A   DAAEA R GL+   +
Sbjct: 125 GVESAKFSLSEAKLGLVP-AVISPYVSAAIGVRQARRYFASAEVFDAAEAARIGLLHECV 183

Query: 182 PAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERR---LFHSLFATE 238
            A +L          + +    A    K    R    T       +R    L   L  + 
Sbjct: 184 AAEALDATVERLLHMLGKCGPIAQDEAKRLALRVAGITRDGAEQADRENAALIARLRVSA 243

Query: 239 DQKEGMAAFVEKRKPVFKHR 258
           + +EG+ AF++KR P +  R
Sbjct: 244 EGQEGLTAFLDKRAPAWAGR 263


Lambda     K      H
   0.321    0.134    0.380 

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: 154
Number of extensions: 7
Number of successful extensions: 4
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: 258
Length of database: 264
Length adjustment: 25
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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