GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pseudomonas putida KT2440

Align Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate PP_3754 PP_3754 Beta-ketothiolase BktB

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2411
         (393 letters)



>FitnessBrowser__Putida:PP_3754
          Length = 394

 Score =  563 bits (1451), Expect = e-165
 Identities = 284/394 (72%), Positives = 328/394 (83%), Gaps = 1/394 (0%)

Query: 1   MNTPEIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALERAAVDPALVGHLVMGNVIP 60
           M++ EIYVVSA R+AIG FGGSLKD+PLADLA+   +AA+ER+ +    VGH+VMG VIP
Sbjct: 1   MSSAEIYVVSAVRSAIGGFGGSLKDLPLADLASAVTRAAIERSGLAAEQVGHMVMGTVIP 60

Query: 61  TETRDAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAES 120
           TE RDAY++RVAAMNAGIPKETPA+NVNRLCGSGLQAI++AAQ L+LGD D+ V AGAES
Sbjct: 61  TEPRDAYLARVAAMNAGIPKETPAFNVNRLCGSGLQAIVSAAQGLLLGDTDVAVAAGAES 120

Query: 121 MSRGPYLMPAARWGSRMGNAQVIDYMLGILHDPFHGIHMGITAENVAARNGITREMQDAL 180
           MSRGPYL+P ARWG+RMG+ Q IDY +G+L DPF   HMGITAENV+A+ GITREMQD L
Sbjct: 121 MSRGPYLLPQARWGARMGDLQGIDYTVGVLQDPFQHFHMGITAENVSAKYGITREMQDEL 180

Query: 181 AFEDQQRAAHAIANGYFSEQIATVEIQDRKGVKLFSVDEHPRA-TSLEQLAAMKPAFKKD 239
           A   Q+RAA AIA G F+ QI  +E++ RKG   FSVDEH RA  + EQLA MKP FKKD
Sbjct: 181 ALTSQRRAARAIAEGRFASQIVALELKTRKGSVQFSVDEHVRADVTAEQLAGMKPVFKKD 240

Query: 240 GSVTAGNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIPATRL 299
           G+VTAGNASG+NDGAA LV+A+G+AV+   LKPLARLV YAHAGVEPE MGLGPIPATR 
Sbjct: 241 GTVTAGNASGINDGAAGLVLATGDAVRRLGLKPLARLVGYAHAGVEPELMGLGPIPATRK 300

Query: 300 ALKRAGLTVADLDVIEANIAFAAQACAVSQELDLDPAKVNPNGSGIALGHPVGATGAIIA 359
            L++ GL + DLDVIE+N AFAAQACAV++EL  DP KVNPNGSGI+LGHPVGATGAIIA
Sbjct: 301 VLEKTGLNLQDLDVIESNEAFAAQACAVARELGFDPEKVNPNGSGISLGHPVGATGAIIA 360

Query: 360 TKAIHELHRTGGRYALVTMCIGGGQGIAAIFERV 393
           TKAIHEL R  GRYAL TMCIGGGQGIA +FERV
Sbjct: 361 TKAIHELQRIQGRYALATMCIGGGQGIAVVFERV 394


Lambda     K      H
   0.318    0.133    0.378 

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: 520
Number of extensions: 23
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: 393
Length of database: 394
Length adjustment: 31
Effective length of query: 362
Effective length of database: 363
Effective search space:   131406
Effective search space used:   131406
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