GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Nocardioides daejeonensis MJ31

Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate WP_110204929.1 DNK54_RS00015 acetyl-CoA C-acetyltransferase

Query= SwissProt::P09110
         (424 letters)



>NCBI__GCF_003194585.1:WP_110204929.1
          Length = 395

 Score =  244 bits (624), Expect = 3e-69
 Identities = 152/396 (38%), Positives = 219/396 (55%), Gaps = 19/396 (4%)

Query: 39  VVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGAGA 98
           V+V G RT + R   GG KD +  +L    +   L+   +  +Q+  + +G+V+Q GAG 
Sbjct: 5   VIVAGARTPVGRL-LGGLKDLSAADLGGVAIKGALEKAGISGDQVDYVVMGHVIQAGAGQ 63

Query: 99  IMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSLADR 158
           I AR A     IP  VP  T+N+ C SG+ A+A     IR G ++I +A G+ESM+ A  
Sbjct: 64  ITARQAAVKGGIPMGVPSLTINKVCLSGINAIALADQLIRAGEHEIVVAGGMESMTQAPH 123

Query: 159 GNPGNITSRLMEKEKARDCLIPMGITSENVAERFG------------ISREKQDTFALAS 206
             P +         K  D +    +  +   +  G            ++RE+QD F+  S
Sbjct: 124 LLPKSREGFKYGDTKLVDSMAYDALYDQFTDQAMGNLTEQCNVAGGNLTREEQDAFSARS 183

Query: 207 QQKAARAQSKGCFQAEIVPVTTTVHDDKGTKRSITVTQDEGIRPSTTMEGLAKLKPAFKK 266
            Q AA AQ  G F  EIVPVT +       +  + V+ DEG+R  TT E L  L+PAF K
Sbjct: 184 HQLAAAAQKNGVFDDEIVPVTIS-----SRRGDVVVSVDEGVRGDTTAESLGGLRPAFAK 238

Query: 267 DGSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIP 326
           DG+ TAG+SSQ+SDGA A+++  ++KAEELGL  L  + +   V  P   + + PA AI 
Sbjct: 239 DGTITAGSSSQISDGACAVVVMSKAKAEELGLEWLAEIGASGQVAGPDSTLQLQPARAIA 298

Query: 327 VALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQ 386
            A++K G+ VSD+D+FE+NEAFA+       +L +  +KVN  GGA+A+GHP+G +GAR 
Sbjct: 299 KAVEKEGIAVSDIDLFELNEAFAAVGIESARELGVSEDKVNVNGGAIAIGHPVGMSGARI 358

Query: 387 VITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFEYP 422
           V+ L  ELKRRG    G  ++C G G G A +   P
Sbjct: 359 VLHLALELKRRG-GGIGAAALCGGGGQGDALIVRVP 393


Lambda     K      H
   0.317    0.134    0.385 

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: 495
Number of extensions: 25
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: 424
Length of database: 395
Length adjustment: 31
Effective length of query: 393
Effective length of database: 364
Effective search space:   143052
Effective search space used:   143052
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 (21.7 bits)
S2: 50 (23.9 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