GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Pseudomonas fluorescens GW456-L13

Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate PfGW456L13_2157 3-ketoacyl-CoA thiolase (EC 2.3.1.16)

Query= SwissProt::P09110
         (424 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2157
          Length = 394

 Score =  286 bits (733), Expect = 6e-82
 Identities = 169/391 (43%), Positives = 238/391 (60%), Gaps = 9/391 (2%)

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

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

Query: 156 ADRG-NPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQ 214
             +  N  N+ + L+ KE+      PMG T+E VA R+ +SR++QD +AL SQQ+ A AQ
Sbjct: 123 TMKSVNTDNLINPLL-KEQVPGIYFPMGQTAEIVARRYNVSRQEQDLYALQSQQRTAEAQ 181

Query: 215 SKGCFQAEIVPVTTTVH-DDKGTKRSIT----VTQDEGIRPSTTMEGLAKLKPAFKKDGS 269
           + G F  EIVP++     +DK T ++      V +D+  RP TT+E L  LKP F +DGS
Sbjct: 182 AAGLFTDEIVPMSVKYRVEDKATGQAQILDGIVDRDDCNRPDTTLESLTGLKPVFAEDGS 241

Query: 270 TTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVAL 329
            TAGNSSQ+SDGA+  L+    KA ELGL      R + V G  PD MGIGP +++P  L
Sbjct: 242 VTAGNSSQLSDGASMTLVMSLEKALELGLKPKAFFRGFTVAGCAPDEMGIGPVFSVPKLL 301

Query: 330 QKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVIT 389
           +  GL ++D+D++E+NEAFASQ  Y   +L +   + N  GG++++GHP G TG+RQV  
Sbjct: 302 KAKGLRIADIDLWELNEAFASQCLYSRNRLEIDNARYNVNGGSISIGHPFGMTGSRQVGH 361

Query: 390 LLNELKRRGKRAYGVVSMCIGTGMGAAAVFE 420
           L+ EL+RR  R YG+V+MC+G GMGA  +FE
Sbjct: 362 LVRELQRRNLR-YGIVTMCVGGGMGATGLFE 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: 423
Number of extensions: 18
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