GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Cupriavidus basilensis 4G11

Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate RR42_RS23050 RR42_RS23050 4-oxalomesaconate tautomerase

Query= SwissProt::A0A0U2X0E4
         (443 letters)



>FitnessBrowser__Cup4G11:RR42_RS23050
          Length = 359

 Score =  273 bits (697), Expect = 8e-78
 Identities = 159/340 (46%), Positives = 205/340 (60%), Gaps = 9/340 (2%)

Query: 1   MLHPIDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSK 60
           M   I   + R GTSRG  F A  LP +P+ RD  L+S MGS H LQ+DG+GGG+SLTSK
Sbjct: 1   MSKDIPCVLMRGGTSRGPLFRADWLPDDPARRDQVLLSAMGSPHALQVDGLGGGSSLTSK 60

Query: 61  VAIVSASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTT 120
            AIVS S +R   D+DYLF QV + +  VDT PNCGN+++ VA FAIE GLV+     TT
Sbjct: 61  AAIVSCS-RRPGCDIDYLFAQVAVDKHRVDTRPNCGNMLAAVAPFAIEEGLVRAGQCATT 119

Query: 121 CLVRIFNLNSRQASELVIPVYNGRVHYDDIDDMH-MQRPSARVGLRFLDTVGSCTGKLLP 179
             +RIFN+N+    E V+    G+V Y     +  +   +A + L FLD  G  TG + P
Sbjct: 120 --LRIFNVNTSSVVEAVVQTPGGQVTYAGATRIDGVAGTAAPIMLNFLDAWGRVTGAMFP 177

Query: 180 TGNASDWIDGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLEAGR 239
           TGN  D ID + V+ ID+A+P+V +    +G+ G E PA L+AN  +L RLE VR +AGR
Sbjct: 178 TGNTIDVIDAVPVTCIDAAMPLVVVHAASLGVRGDETPAALDANREMLARLESVRRQAGR 237

Query: 240 RMGLGDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDGSVV 299
           RMGLGDVS SV+PK  L+         T+RYFTP  CH AHAVTGA+  A AAY     V
Sbjct: 238 RMGLGDVSHSVIPKPVLVSGCGRANEITSRYFTPLRCHTAHAVTGAVGIA-AAYCTPGTV 296

Query: 300 CEILSSRASACSASQRRISIEHPSGVLEVGLVPPENAAQS 339
              L+S  S     Q RI + HP+G +EV + P  +   S
Sbjct: 297 ANGLASTPS----PQGRIVVRHPAGSIEVHVEPERDGGPS 332


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: 421
Number of extensions: 18
Number of successful extensions: 5
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