GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Pseudomonas stutzeri RCH2

Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate GFF1790 Psest_1829 acetyl-CoA acetyltransferases

Query= SwissProt::P09110
         (424 letters)



>FitnessBrowser__psRCH2:GFF1790
          Length = 394

 Score =  285 bits (728), Expect = 2e-81
 Identities = 170/390 (43%), Positives = 239/390 (61%), Gaps = 7/390 (1%)

Query: 37  DVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGA 96
           +VV+V   RT + ++ RG F  T PD++ +  + A+L   +L P  + D  VG     GA
Sbjct: 3   EVVIVDSVRTGLAKSFRGKFNMTRPDDMAAHCVDALLSRNDLDPALVEDCIVGAGSNEGA 62

Query: 97  -GAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSL 155
            G  + R    LS +       T+NR CSSGLQA+A  A  I +G  DI +A GVES++L
Sbjct: 63  QGYNIGRNVAVLSRLGIGCAGMTLNRYCSSGLQAIAVAANQIASGCSDIIVAGGVESITL 122

Query: 156 ADRGNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQS 215
             +    +     + +E+       MG T+E VA R+ ++RE+QD ++L SQQ+ ARAQ+
Sbjct: 123 TLKSRNTDHLFNPIIQERVPGIYHTMGQTAELVARRYNVTREQQDLYSLQSQQRTARAQA 182

Query: 216 KGCFQAEIVPVTTTVH-DDKGT-KRSI---TVTQDEGIRPSTTMEGLAKLKPAFKKDGST 270
           +G F+ EIVP+      +DK T +R++    V  D+  RP TT+E LA LKP F +DGS 
Sbjct: 183 EGLFRDEIVPMNVQYFTEDKNTGERTVHEGVVDADDCNRPDTTLESLAGLKPVFAEDGSV 242

Query: 271 TAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVALQ 330
           TAGN+SQ+SDGA+  L+    KA ELGL      R + V G  P+ MGIGP YA+P  L+
Sbjct: 243 TAGNASQLSDGASMTLVMSLDKAIELGLKPRAFFRGFTVAGCEPEEMGIGPVYAVPRLLK 302

Query: 331 KAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVITL 390
             GL V+D+D++E+NEAFASQ  YC + L +  EK N  GG++++GHP G TG+R    L
Sbjct: 303 AKGLQVADIDLWELNEAFASQCLYCRDTLGIDNEKYNVNGGSISIGHPFGMTGSRTAGHL 362

Query: 391 LNELKRRGKRAYGVVSMCIGTGMGAAAVFE 420
           + EL+RR  R YGVV+MC+G GMGAA +FE
Sbjct: 363 IRELQRRELR-YGVVTMCVGGGMGAAGLFE 391


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: 428
Number of extensions: 25
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: 424
Length of database: 394
Length adjustment: 31
Effective length of query: 393
Effective length of database: 363
Effective search space:   142659
Effective search space used:   142659
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 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:

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