GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdA in Dinoroseobacter shibae DFL-12

Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate 3608766 Dshi_2158 Pyruvate dehydrogenase (acetyl-transferring) (RefSeq)

Query= BRENDA::Q72GU1
         (367 letters)



>lcl|FitnessBrowser__Dino:3608766 Dshi_2158 Pyruvate dehydrogenase
           (acetyl-transferring) (RefSeq)
          Length = 331

 Score =  154 bits (388), Expect = 4e-42
 Identities = 106/318 (33%), Positives = 159/318 (50%), Gaps = 4/318 (1%)

Query: 36  EKLRRLYRDMLAARMLDERYTILIRTGKTS-FIAPAAGHEAAQVAIAHAIRPGFDWVFPY 94
           E L   YR+ML  R  +E+   L   G    F     G EA  V +  A   G D     
Sbjct: 15  EDLMSYYREMLLIRRFEEKAGQLYGMGLIGGFCHLYIGQEAVVVGLEAAAEDG-DKRVTS 73

Query: 95  YRDHGLALALGIPLKELFGQMLATKADPNKGRQMPEHPGSKALNFFTVASPIASHVPPAA 154
           YRDHG  LA G+  K +  ++   +   +KG+    H  SK  +F+     + + VP  A
Sbjct: 74  YRDHGHMLACGMDPKGVMAELTGREGGYSKGKGGSMHMFSKEKHFYGGHGIVGAQVPIGA 133

Query: 155 GAAISMKLLRTGQVAVCTFGDGATSEGDWYAGINFAAVQGAPAVFVCENNFYAISVDYRH 214
           G A S K     +V    FGDGA ++G  Y   N A +   P VFV ENN YA+      
Sbjct: 134 GLAFSDKYRGNDRVTFAYFGDGAANQGQVYETYNMAELWMLPVVFVIENNQYAMGTSVAR 193

Query: 215 QTHSPTIADKAHAFGIPGYLVDGMDVLASYYVVKEAVERARRGEGPSLVELRVYRYGPHS 274
            T SP++ ++  A+GIPG  VDGMDVLA     ++AV   R G+GP ++E++ YRY  HS
Sbjct: 194 STKSPSLWERGAAYGIPGEEVDGMDVLAVKAAGEKAVAHCRAGKGPYILEVKTYRYRGHS 253

Query: 275 SADDDSRYRPKEEVAFWR-KKDPIPRFRRFLEARGLWNEEWEEDVREEIRAELERGLKEA 333
            + D ++YR +EEV   R ++D I   R  L +    +E+  + + +EI+A +    + +
Sbjct: 254 MS-DPAKYRTREEVQKVREQRDAIEHVREMLLSGNHASEDELKAIDKEIKAVVNEAAEFS 312

Query: 334 EEAGPVPPEWMFADVFAE 351
            E+       ++ D++AE
Sbjct: 313 RESPEPALSELWTDIYAE 330


Lambda     K      H
   0.320    0.138    0.426 

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: 317
Number of extensions: 22
Number of successful extensions: 1
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: 367
Length of database: 331
Length adjustment: 29
Effective length of query: 338
Effective length of database: 302
Effective search space:   102076
Effective search space used:   102076
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: 49 (23.5 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 preprint 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