GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Pseudomonas putida KT2440

Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate PP_2055 PP_2055 putative isomerase

Query= SwissProt::A0A0U2X0E4
         (443 letters)



>FitnessBrowser__Putida:PP_2055
          Length = 359

 Score =  277 bits (708), Expect = 4e-79
 Identities = 163/359 (45%), Positives = 220/359 (61%), Gaps = 10/359 (2%)

Query: 5   IDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIV 64
           I   + R GTS+G +F A DLPA   ERD  LI++MGSGH L+IDG+GGG+  TSKVAI+
Sbjct: 4   IPCVLMRGGTSKGPFFHAWDLPANVVERDELLINLMGSGHELEIDGIGGGSPQTSKVAII 63

Query: 65  SASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVR 124
           S S   ++ DVDYLF QV + +R VDTAPNCGN++  V  FAIE+GLV+     T  LVR
Sbjct: 64  SPSLH-ADADVDYLFVQVMVAQRRVDTAPNCGNMLCAVGPFAIEQGLVKGQEGKT--LVR 120

Query: 125 IFNLNSRQASELVIPVYNGRVHYDDIDDMH-MQRPSARVGLRFLDTVGSCTGKLLPTGNA 183
           I NLN+      ++    G V Y+    +  +   +A V L FLD VGS TGKL PTG A
Sbjct: 121 IRNLNTGTFVNSLVETPGGIVRYEGRTAIDGVPGTAAPVHLTFLDAVGSKTGKLFPTGKA 180

Query: 184 SDWIDGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLEAGRRMGL 243
            D IDG+ V+ ID A+P++ +    +G++GSE PA L+AN+ALL+RLE +RL+AG+ MGL
Sbjct: 181 QDVIDGVPVTCIDMAMPMMVVEASQLGVSGSETPAQLDANSALLERLEALRLKAGKAMGL 240

Query: 244 GDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDGSVVCEIL 303
           GDVSG V+PK  L+       T   RYF P  CH A A+TGA+  A A    G+V+ ++L
Sbjct: 241 GDVSGMVIPKPVLVSKPRYDGTLQVRYFMPHNCHRALAITGAVGLATACVSPGTVIADLL 300

Query: 304 SSRASACSASQRRISIEHPSGVLEVGLVPPENAAQSLVDVAVVERSVALIAHARVYYTT 362
              A   +    ++ +EHPSG ++V L    + A+     A V R+   +    VY  T
Sbjct: 301 GEGAQQLA----QVRLEHPSGGIDVALT--RSGAEGQTIQASVVRTARRLFSGFVYAPT 353


Lambda     K      H
   0.318    0.133    0.389 

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: 382
Number of extensions: 16
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: 443
Length of database: 359
Length adjustment: 31
Effective length of query: 412
Effective length of database: 328
Effective search space:   135136
Effective search space used:   135136
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