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 16795 b2711 nitric oxide reductase (NCBI)

Query= SwissProt::Q84BZ0
         (406 letters)



>FitnessBrowser__Keio:16795
          Length = 377

 Score =  111 bits (277), Expect = 4e-29
 Identities = 96/311 (30%), Positives = 148/311 (47%), Gaps = 21/311 (6%)

Query: 7   VIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDA 66
           VI+G+G AAR+  + +R +DA  P+ +I A+    Y++P LS   +++         R  
Sbjct: 6   VIIGSGFAARQLVKNIRKQDATIPLTLIAADSMDEYNKPDLSH--VISQGQRADDLTRQT 63

Query: 67  AWYDAQRIALRL--GTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGV 124
           A   A++  L L   T V  I+ EA+ V+        Y KLVLATG+    F  P+    
Sbjct: 64  AGEFAEQFNLHLFPQTWVTDIDAEARVVK-SQNNQWQYDKLVLATGASA--FVPPVPGRE 120

Query: 125 VAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRA 184
           +   + +  + RA   QL   RRV ++GGG IG E+A    + G  VT+ID AA +L   
Sbjct: 121 LMLTLNSQQEYRACETQLRDARRVLIVGGGLIGSELAMDFCRAGKAVTLIDNAASILASL 180

Query: 185 L-PEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLP 243
           + PEV     HRL  E GV   + +  + +     G       + ++  D V+   G+ P
Sbjct: 181 MPPEVSSRLQHRL-TEMGVHLLLKSQLQGLEKTDSGIQATLDRQRNIEVDAVIAATGLRP 239

Query: 244 NVELAQAAGLDVDNGIRVDAGCRTADRAIFAAG---EVTMHFNPLLGRHVRIESWQVAEN 300
              LA+ AGL ++ G+ VD+  +T++  I+A G   E+     P L         Q  + 
Sbjct: 240 ETALARRAGLTINRGVCVDSYLQTSNTDIYALGDCAEINGQVLPFL---------QPIQL 290

Query: 301 QPAVAAANLLG 311
              V A NLLG
Sbjct: 291 SAMVLAKNLLG 301


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: 235
Number of extensions: 15
Number of successful extensions: 2
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: 377
Length adjustment: 31
Effective length of query: 375
Effective length of database: 346
Effective search space:   129750
Effective search space used:   129750
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