GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Escherichia coli BW25113

Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate 14894 b0769 hypothetical protein (NCBI)

Query= SwissProt::A0A0U2X0E4
         (443 letters)



>FitnessBrowser__Keio:14894
          Length = 350

 Score =  264 bits (674), Expect = 4e-75
 Identities = 160/356 (44%), Positives = 213/356 (59%), Gaps = 12/356 (3%)

Query: 5   IDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIV 64
           I   + R GTSRG + LA  LP + ++RD  L++IMGSG+ L+IDG+GGGN LTSKVAI+
Sbjct: 4   IPCVMMRGGTSRGAFLLAEHLPEDQTQRDKILMAIMGSGNDLEIDGIGGGNPLTSKVAII 63

Query: 65  SASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVR 124
           S S+     DVDYLF QV + E+ VDT PNCGN++SGV AFAIE GL+      T   VR
Sbjct: 64  SRSSD-PRADVDYLFAQVIVHEQRVDTTPNCGNMLSGVGAFAIENGLIAATSPVTR--VR 120

Query: 125 IFNLNSRQASELVIPVYNGRVHYDDIDDMH-MQRPSARVGLRFLDTVGSCTGKLLPTGNA 183
           I N+N+    E  +   NG V Y+    +  +   +A V L FL+  G+ TGK+ PT N 
Sbjct: 121 IRNVNTGTFIEADVQTPNGVVEYEGSARIDGVPGTAAPVALTFLNAAGTKTGKVFPTDNQ 180

Query: 184 SDWIDGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLEAGRRMGL 243
            D+ D + V+ ID A+PVV I    +G TG E PA L+A+ ALL R+E +RL+AG+ MGL
Sbjct: 181 IDYFDDVPVTCIDMAMPVVIIPAEYLGKTGYELPAELDADKALLARIESIRLQAGKAMGL 240

Query: 244 GDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDGSVVCEIL 303
           GDVS  V+PK  LI P  +      RYF P +CH A A+TGAI  + +  ++G+V  +I+
Sbjct: 241 GDVSNMVIPKPVLISPAQKGGAINVRYFMPHSCHRALAITGAIAISSSCALEGTVTRQIV 300

Query: 304 SSRASACSASQRRISIEHPSGVLEVGLVPPENAAQSLVDVAVVERSVALIAHARVY 359
                  S     I+IEHPSG L+V L      A +L   A V R+   I    VY
Sbjct: 301 P------SVGYGNINIEHPSGALDVHLSNEGQDATTL--RASVIRTTRKIFSGEVY 348


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: 384
Number of extensions: 13
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: 350
Length adjustment: 31
Effective length of query: 412
Effective length of database: 319
Effective search space:   131428
Effective search space used:   131428
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