GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Pseudomonas fluorescens FW300-N1B4

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate Pf1N1B4_3234 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)

Query= uniprot:D8ITH5
         (401 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3234
          Length = 400

 Score =  564 bits (1453), Expect = e-165
 Identities = 282/399 (70%), Positives = 335/399 (83%), Gaps = 1/399 (0%)

Query: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61
           +  ICDAIRTP GR+GG L AVRADDLAA PI++LM RNP VDWS V+++  GCANQAGE
Sbjct: 3   DVYICDAIRTPIGRFGGGLSAVRADDLAAVPIKALMARNPSVDWSAVDEVFLGCANQAGE 62

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

Query: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181
           APFVMGKA++AF+R+  + DTTIGWRF+NPLMKAQYG+D+MP+TA+NVA D++I+RADQD
Sbjct: 123 APFVMGKADAAFSRNMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYRISRADQD 182

Query: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241
           AFALRSQQR AAAQAAGFFA EI  + I  KKG+  VVT DEHPR DTTL TLAKLK V 
Sbjct: 183 AFALRSQQRTAAAQAAGFFAEEIVEVRIAHKKGES-VVTQDEHPRADTTLETLAKLKPVN 241

Query: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301
            PD TVTAGNASGVNDGA AL+LAS +A   + L  RA+VLGM++AGVAPR+MG GP PA
Sbjct: 242 GPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARAKVLGMSSAGVAPRVMGIGPVPA 301

Query: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361
           VRK+  ++GL ++  DVIELNEAFA+QGLAV+R+LGL DD+A VNPNGGAIA+GHPLG S
Sbjct: 302 VRKLTERLGLAVSDFDVIELNEAFASQGLAVLRELGLADDSAQVNPNGGAIALGHPLGMS 361

Query: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
           GARLV TA++QLE++GG+  L TMC+GVGQG+AL IERV
Sbjct: 362 GARLVLTALHQLEKTGGKKGLATMCVGVGQGLALAIERV 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: 552
Number of extensions: 20
Number of successful extensions: 2
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.

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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