GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Pseudomonas putida KT2440

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate PP_2335 PP_2335 methylcitrate synthase

Query= BRENDA::Q9I5E3
         (375 letters)



>FitnessBrowser__Putida:PP_2335
          Length = 375

 Score =  673 bits (1737), Expect = 0.0
 Identities = 332/375 (88%), Positives = 348/375 (92%)

Query: 1   MAEAKVLSGAGLRGQVAGQTALSTVGQEGAGLTYRGYDVRDLAAAAIFEEVAYLLLYGEL 60
           MAEAKVLSGAGLRGQVAGQTALSTVGQ GAGLTYRGYDVRDLAA A FEEVAYLLLYGEL
Sbjct: 1   MAEAKVLSGAGLRGQVAGQTALSTVGQAGAGLTYRGYDVRDLAAGAEFEEVAYLLLYGEL 60

Query: 61  PNKQQLDAYLKKLQGQRDLPQALKEVLERIPKDAHPMDVMRTGASVLGTLEPELSFDQQR 120
           P + +L  Y +KL+G RDLPQALKEVLERIP+DAHPMDVMRTG SVLGTLEPEL+F+ QR
Sbjct: 61  PTQAELADYKRKLKGLRDLPQALKEVLERIPRDAHPMDVMRTGCSVLGTLEPELTFEAQR 120

Query: 121 DVADRLLAAFPAIMTYWYRFTHEGQRIDCNSDEPTIGGHFLALLHGKKPSELHVKVMNVS 180
           D  DRLLA FPA+M YWYRFTH G RIDC +DE T+GGHFL LLHGKKPSELHVKVMNVS
Sbjct: 121 DKTDRLLALFPAVMCYWYRFTHHGVRIDCTTDEDTLGGHFLHLLHGKKPSELHVKVMNVS 180

Query: 181 LILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIERFSSPQ 240
           LILYAEHEFNASTFTARVCASTLSDLYSCVT AIGSLRGPLHGGANEAAMELIERF SPQ
Sbjct: 181 LILYAEHEFNASTFTARVCASTLSDLYSCVTAAIGSLRGPLHGGANEAAMELIERFQSPQ 240

Query: 241 EATAELLKMLERKDKIMGFGHAIYKDSDPRNEVIKGWSKQLADEVGDKVLFAVSEAIDKT 300
           EATAELL+MLERKDKIMGFGHAIYK+SDPRNEVIKGWSKQLADEVGDKVL+ VSEAIDKT
Sbjct: 241 EATAELLRMLERKDKIMGFGHAIYKESDPRNEVIKGWSKQLADEVGDKVLYPVSEAIDKT 300

Query: 301 MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQRANNRIIRPSAE 360
           MWEQK+LFPNADFYHASAYHFMGIPTKLFTPIFVCSR +GW AHVFEQRANNRIIRPSAE
Sbjct: 301 MWEQKRLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRANNRIIRPSAE 360

Query: 361 YTGVEQRAFVPLEQR 375
           Y GVEQR FVP+EQR
Sbjct: 361 YVGVEQRQFVPIEQR 375


Lambda     K      H
   0.319    0.134    0.396 

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: 580
Number of extensions: 12
Number of successful extensions: 1
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: 375
Length of database: 375
Length adjustment: 30
Effective length of query: 345
Effective length of database: 345
Effective search space:   119025
Effective search space used:   119025
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