GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdA in Pseudomonas putida KT2440

Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate PP_0555 PP_0555 Acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit alpha

Query= metacyc::MONOMER-11683
         (330 letters)



>lcl|FitnessBrowser__Putida:PP_0555 PP_0555
           Acetoin:2,6-dichlorophenolindophenol oxidoreductase
           subunit alpha
          Length = 325

 Score =  155 bits (393), Expect = 1e-42
 Identities = 103/320 (32%), Positives = 165/320 (51%), Gaps = 5/320 (1%)

Query: 11  LTDQEAVDMYRTMLLARKIDERMWLLNRSGKIP-FVISCQGQEAAQVGAAFALDREMDYV 69
           L+ ++ +  Y  M   R  +ER+ +   +G+IP FV    G+EA+  G    L R+ D +
Sbjct: 5   LSTEQLLHAYEVMRTIRAFEERLHVEFATGEIPGFVHLYAGEEASAAGVMAHL-RDSDCI 63

Query: 70  LPYYRDMGVVLAFGMTAKDLMMSGFAKAADPNSGGRQMPGHFGQKKNRIVTGSSPVTTQV 129
              +R  G  +A G+    +M   + K      GG+    H    +  ++  +  V    
Sbjct: 64  ASTHRGHGHCIAKGVDVYGMMAEIYGKKTGV-CGGKGGSMHIADLEKGMLGANGIVGAGA 122

Query: 130 PHAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYAISV 189
           P   G ALA +++ +D  +   FG+G+SN+G   E  N A++  LP IF+ ENN YA + 
Sbjct: 123 PLVAGAALAAKLKGRDDVSVAFFGDGASNEGAVFEAMNMASIMNLPCIFVAENNGYAEAT 182

Query: 190 PYDKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETISYRL 249
             +  VAC++I+DRA G+GMPGVT++G D   VY+A   A ERAR G+GP+LIE    R 
Sbjct: 183 ASNWSVACDHIADRAAGFGMPGVTIDGFDFFAVYEAAGAAIERARSGQGPSLIEVKLSRY 242

Query: 250 TPHSSDDDDSSYRGREEVEEAKKS-DPLLTYQAYLKETGLLSDEIEQTMLDEIMAIVNEA 308
             H  + D  +YR  +EV+  ++S D L+ ++      GLL+ E    +   +  ++ +A
Sbjct: 243 YGH-FEGDAQTYRAPDEVKNLRESRDCLMQFRNKTTRAGLLTAEQLDAIDARVEDLIEDA 301

Query: 309 TDEAENAPYAAPESALDYVY 328
              A++ P   P   L  VY
Sbjct: 302 VRRAKSDPKPQPADLLTDVY 321


Lambda     K      H
   0.316    0.132    0.377 

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: 233
Number of extensions: 14
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: 330
Length of database: 325
Length adjustment: 28
Effective length of query: 302
Effective length of database: 297
Effective search space:    89694
Effective search space used:    89694
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 (21.6 bits)
S2: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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