GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Erythrobacter marinus HWDM-33

Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate WP_082126407.1 AAV99_RS09615 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha

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



>NCBI__GCF_001013305.1:WP_082126407.1
          Length = 368

 Score =  156 bits (394), Expect = 9e-43
 Identities = 106/314 (33%), Positives = 165/314 (52%), Gaps = 11/314 (3%)

Query: 12  TDQEAVDMYRTMLLARKIDERMWLLNRSGKIP-FVISCQGQEAAQVGAAFALDREMDYVL 70
           +D++ +  Y  MLL R+ +E+   L   G I  F     GQEA  +G   ALD ++D V+
Sbjct: 49  SDEQLLHFYEQMLLIRRFEEKAGQLYGLGLIGGFCHLYIGQEAVAIGLQSALDSDVDSVI 108

Query: 71  PYYRDMGVVLAFGMTAKDLM--MSGFAKAADPNSGGRQMPGHFGQKKNRIVTGSSPVTTQ 128
             YRD G +LA+G+    +M  ++G A       GG     H    +++   G   V  Q
Sbjct: 109 TGYRDHGHMLAYGIDPNVIMAELTGRAAGISKGKGGSM---HMFSTEHKFYGGHGIVGAQ 165

Query: 129 VPHAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYAIS 188
           V    G+A+A +           FG+G++NQG  +E  N AA+ KLP++F+ ENN+YA+ 
Sbjct: 166 VSLGGGLAMAHQYRGDGGLCLAYFGDGAANQGQVYETMNMAALWKLPMVFVVENNQYAMG 225

Query: 189 VPYDKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETISYR 248
              ++  A      R   + +PG+ VNG D LEV QA + A +  R G GP L+E  +YR
Sbjct: 226 TAVNRSSAETEFYRRGTAFRIPGMEVNGMDVLEVRQAAEIAFKYVREGNGPVLMECNTYR 285

Query: 249 LTPHSSDDDDSSYRGREEVEEAKKS-DPLLTYQAYLKETGLLSDEIEQTMLDE-IMAIVN 306
              HS   D + YR REEV++ +++ DP+   +  L   GL  D+ +   +D+ I A+V+
Sbjct: 286 YRGHSM-SDPAKYRTREEVQDQRENHDPIERLKKELNTAGL--DDAKLKEIDKGIRAVVS 342

Query: 307 EATDEAENAPYAAP 320
            A D +E++P   P
Sbjct: 343 AAADFSESSPEPQP 356


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: 260
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: 330
Length of database: 368
Length adjustment: 29
Effective length of query: 301
Effective length of database: 339
Effective search space:   102039
Effective search space used:   102039
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: 49 (23.5 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