GapMind for catabolism of small carbon sources

 

Alignments for a candidate for andAa in Escherichia coli BW25113

Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate 16641 b2542 phenylpropionate dioxygenase, ferredoxin reductase subunit (NCBI)

Query= SwissProt::Q84BZ0
         (406 letters)



>FitnessBrowser__Keio:16641
          Length = 400

 Score =  212 bits (540), Expect = 1e-59
 Identities = 146/406 (35%), Positives = 202/406 (49%), Gaps = 9/406 (2%)

Query: 1   MSADPFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQR 60
           M     +IVG G AA   A +LR +     + +   ER LPY+RP LSK  LL +D  Q 
Sbjct: 1   MKEKTIIIVGGGQAAAMAAASLRQQGFTGELHLFSDERHLPYERPPLSKSMLL-EDSPQL 59

Query: 61  AFVRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPI 120
             V  A W+    + L  G  +  + R+ + + L +G +  + +L +ATG+  R      
Sbjct: 60  QQVLPANWWQENNVHLHSGVTIKTLGRDTRELVLTNGESWHWDQLFIATGAAARPLPLLD 119

Query: 121 DAGVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARL 180
             G     +R   DA  LR  L   R V ++G G IGLE+AA+A Q  C VTVI+ AA +
Sbjct: 120 ALGERCFTLRHAGDAARLREVLQPERSVVIIGAGTIGLELAASATQRRCKVTVIELAATV 179

Query: 181 LQRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGD--VHADVVVVG 238
           + R  P  V  Y  + H + GV      L  AI     G  +  T +    + ADVV+ G
Sbjct: 180 MGRNAPPPVQRYLLQRHQQAGVRI---LLNNAIEHVVDGEKVELTLQSGETLQADVVIYG 236

Query: 239 IGVLPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVA 298
           IG+  N +LA+ A LD  NGI +D  CRT D AIFA G+V +        H R ESW+ A
Sbjct: 237 IGISANEQLAREANLDTANGIVIDEACRTCDPAIFAGGDVAITRLDNGALH-RCESWENA 295

Query: 299 ENQPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFG 358
            NQ  +AAA +LG        PW WSDQY  NLQ +G    G   + RG+P       F 
Sbjct: 296 NNQAQIAAAAMLGLPLPLLPPPWFWSDQYSDNLQFIGDM-RGDDWLCRGNPETQKAIWFN 354

Query: 359 LGGDGRIVAAAAVNLGRDIGAARRLIAAGAMPDPQQLADPTVGLKT 404
           L  +G ++ A  +N GR+I   R+ I +G   D + L D  + LK+
Sbjct: 355 L-QNGVLIGAVTLNQGREIRPIRKWIQSGKTFDAKLLIDENIALKS 399


Lambda     K      H
   0.322    0.138    0.410 

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: 340
Number of extensions: 14
Number of successful extensions: 4
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: 406
Length of database: 400
Length adjustment: 31
Effective length of query: 375
Effective length of database: 369
Effective search space:   138375
Effective search space used:   138375
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 (21.9 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