GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Pseudomonas putida KT2440

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate PP_1377 PP_1377 beta-ketoadipyl-CoA thiolase

Query= uniprot:D8ITH5
         (401 letters)



>FitnessBrowser__Putida:PP_1377
          Length = 400

 Score =  567 bits (1460), Expect = e-166
 Identities = 279/399 (69%), Positives = 337/399 (84%), Gaps = 1/399 (0%)

Query: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61
           +  ICDAIRTP GR+GGAL +VRADDLAA P+++L+ERNPGV W +V+++ +GCANQAGE
Sbjct: 3   DVFICDAIRTPIGRFGGALASVRADDLAAVPLKALIERNPGVQWDQVDEVFFGCANQAGE 62

Query: 62  DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121
           DNRNVARMA LLAGLP ++PG T+NRLC S +DAVG A RAI SGE++L+IAGGVESM+R
Sbjct: 63  DNRNVARMALLLAGLPESIPGVTLNRLCASGMDAVGTAFRAIASGEMELVIAGGVESMSR 122

Query: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181
           APFVMGKAESA++R+  + DTTIGWRF+NPLMK+QYG+DSMPETA+NVA D+Q++RADQD
Sbjct: 123 APFVMGKAESAYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQD 182

Query: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241
           AFALRSQQ+ AAAQAAGFFA EI P+ I  KKG+ ++V  DEH RP+TTL  L KLK V 
Sbjct: 183 AFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE-IIVERDEHLRPETTLEALTKLKPVN 241

Query: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301
            PD TVTAGNASGVNDGA A++LAS  A   + L PRARVLGMA+ GVAPR+MG GP PA
Sbjct: 242 GPDKTVTAGNASGVNDGAAAMILASAAAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPA 301

Query: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361
           VRK+  ++G+ ++  DVIELNEAFA+QGLAV+R+LG+ DDA  VNPNGGAIA+GHPLG S
Sbjct: 302 VRKLTERLGIAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMS 361

Query: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
           GARLV TA++QLE+SGGR  L TMC+GVGQG+AL IERV
Sbjct: 362 GARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400


Lambda     K      H
   0.320    0.135    0.394 

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: 567
Number of extensions: 20
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: 401
Length of database: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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