GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Lacinutrix algicola AKS293

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_055437058.1 ASC41_RS12920 acetyl-CoA C-acyltransferase

Query= metacyc::MONOMER-15952
         (401 letters)



>NCBI__GCF_001418085.1:WP_055437058.1
          Length = 392

 Score =  254 bits (648), Expect = 4e-72
 Identities = 158/399 (39%), Positives = 232/399 (58%), Gaps = 12/399 (3%)

Query: 3   EALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAGE 62
           E +I+ A RTPIG + GAL+++ A  LGAI +K  + +   L+   V +V+ G   QAG 
Sbjct: 4   EVVIVSAARTPIGSFLGALSTIPAPKLGAIAIKGALEKI-NLNPELVQEVLMGNVVQAGT 62

Query: 63  DNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSR 122
             +  AR AA+ AG+P +VP TT+N++C SG+  V  AA+++  G+A +++AGG+E+MS 
Sbjct: 63  -GQAPARQAAIFAGIPNTVPCTTINKVCASGMKTVMQAAQSIALGDAEIVVAGGMENMSL 121

Query: 123 AP-FVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRADQ 181
            P +   +S   FG  A + D       V+   QQ  G+     +A+  A ++  SR DQ
Sbjct: 122 IPHYFHARSATKFG-PATMVDGMQKDGLVDVYDQQAMGV-----SADACATKYEFSREDQ 175

Query: 182 DAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGTP 241
           DA+A++S  ++AAA   G+   EIV V + QR+G   IV  DE  + +  ++++  L   
Sbjct: 176 DAYAIQSYKRSAAAWEAGKFNNEIVPVAVPQRRGDDVIVTEDEEYK-NVRMDKIPTLRAA 234

Query: 242 FRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPVP 301
           F + G+VTA NAS +NDGA A++L S E A   GLK  A + G A A  EP      P  
Sbjct: 235 FTKEGTVTAANASTINDGAGAMVLMSREKANELGLKVLATIKGYADAAHEPEWFTTAPSI 294

Query: 302 ATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLGM 361
           A  K L   GL + D+D  E NEAF+  GLA ++ LGL  +D  VN NGGA++LGHPLG 
Sbjct: 295 ALPKALNKAGLDIKDVDFFEFNEAFSIVGLANMKILGL--NDSNVNVNGGAVSLGHPLGC 352

Query: 362 SGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400
           SG R++ T L+ LE+   +     +C G G   AL++ER
Sbjct: 353 SGVRILITLLNVLEQNDAKIGAAAICNGGGGASALVLER 391


Lambda     K      H
   0.319    0.134    0.384 

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: 370
Number of extensions: 13
Number of successful extensions: 5
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: 401
Length of database: 392
Length adjustment: 31
Effective length of query: 370
Effective length of database: 361
Effective search space:   133570
Effective search space used:   133570
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: 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