GapMind for catabolism of small carbon sources

 

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

Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate Pf1N1B4_4204 FldA protein

Query= SwissProt::A0A0U2X0E4
         (443 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4204
          Length = 362

 Score =  250 bits (639), Expect = 4e-71
 Identities = 149/327 (45%), Positives = 198/327 (60%), Gaps = 12/327 (3%)

Query: 5   IDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIV 64
           I   + R GTS+G YFLA DLP EPS RD  L+++MGS    QIDG+GG +SLTSKVAI+
Sbjct: 6   IPCLLMRGGTSKGAYFLADDLPQEPSLRDRVLLAVMGSPDARQIDGIGGADSLTSKVAII 65

Query: 65  SASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVR 124
             S+ R++ DVDYLF QV + E  VD   NCGN+++GV  FAIERGLV      T   VR
Sbjct: 66  KPSS-RADADVDYLFAQVLVEEPRVDYGQNCGNILAGVGPFAIERGLVAVTADVTP--VR 122

Query: 125 IFNLNSRQASELVIPVYNGRVHYDD---IDDMHMQRPSARVGLRFLDTVGSCTGKLLPTG 181
           I+  N+ Q +   +P  +G V Y     ID +  Q  +A + + F D  G+  G LLPTG
Sbjct: 123 IYMENTGQIAIAHVPTSDGEVRYHGDARIDGVPGQ--AAPLIVEFEDVAGASCGALLPTG 180

Query: 182 NASDWIDGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLEAGRRM 241
           NA D IDG++V+ +D+ +PVV IR  ++G +G E+PA L+A+ +L  RLE +RL+AG RM
Sbjct: 181 NARDLIDGIEVTCVDNGMPVVLIRAQELGCSGYESPAQLDADASLKQRLESIRLQAGPRM 240

Query: 242 GLGDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDGSVVCE 301
            LGDV    VPK+ LI P       + R F P  CH +  V GA+  A A+ I+GSV   
Sbjct: 241 NLGDVRLRNVPKMCLIAPPQVGGAISTRSFIPHRCHTSIGVFGAVSVAAASLINGSVA-- 298

Query: 302 ILSSRASACSASQRRISIEHPSGVLEV 328
                A       +R+SIEHP+G   V
Sbjct: 299 --EGMAFVEEGDVKRLSIEHPTGEFTV 323


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: 380
Number of extensions: 14
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: 362
Length adjustment: 31
Effective length of query: 412
Effective length of database: 331
Effective search space:   136372
Effective search space used:   136372
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