GapMind for catabolism of small carbon sources

 

Alignments for a candidate for andAa in Porphyrobacter dokdonensis DSW-74

Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate WP_068863709.1 I603_RS07595 FAD-dependent oxidoreductase

Query= SwissProt::Q84BZ0
         (406 letters)



>NCBI__GCF_001677335.1:WP_068863709.1
          Length = 415

 Score =  237 bits (604), Expect = 5e-67
 Identities = 158/407 (38%), Positives = 215/407 (52%), Gaps = 10/407 (2%)

Query: 7   VIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDA 66
           VIVG GH   + A ALR +  +  I+MIG +   PY+RP LSK+ L  D G QR  +R  
Sbjct: 12  VIVGTGHGGAQAAIALRQQGHEGSILMIGRDNAPPYERPPLSKEYLAGDKGFQRIMIRPE 71

Query: 67  AWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGVV- 125
            ++  + IAL+LG  V AI+  A R+ + DG+ + Y KL+ + G   R    P+   V+ 
Sbjct: 72  KFWAEKGIALKLGAAVTAIDAAAHRITISDGSMVTYRKLIWSGGGDPRRL--PVPGAVLP 129

Query: 126 -AHYVRTVADARALRAQLVRG-RRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQR 183
              YVR  +DA  +   L RG  R  V+GGG+IGLE AA  R+LGC V +++   RLL R
Sbjct: 130 GVFYVRDKSDADTMMLALERGASRAVVIGGGYIGLEAAAVLRKLGCEVVLVEMLPRLLAR 189

Query: 184 ALPEVVGAYAHRLHDERGVGFQMATLPRAIRAA-AGGGAIVETDRG-DVHADVVVVGIGV 241
              E +  +    H  +GV  ++ T  +A+    AG    V  D G +V  D+VVVGIG+
Sbjct: 190 VAGEELSRFYAEEHRRQGVDVRLETGVQAVLGEDAGKVTGVRLDNGEEVACDMVVVGIGI 249

Query: 242 LPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHV-RIESWQVAEN 300
           +P V    AAG    NG+ VD  CRT    I+A G+   H N      V R+ES Q A +
Sbjct: 250 VPAVGPLIAAGAAGSNGVDVDEYCRTTLDDIYAIGDCAAHANRYADNAVIRLESVQNAHD 309

Query: 301 QPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLG 360
                A  ++G  +AY  LPW WS+QYD  LQ  GL      TV+RGDP    FTV  L 
Sbjct: 310 MANTVARAIMGEKEAYEALPWFWSNQYDLKLQTAGLNLGYDQTVLRGDPEARKFTVVYL- 368

Query: 361 GDGRIVAAAAVNLGRDIGAARRLIAAG-AMPDPQQLADPTVGLKTFL 406
            +G  +A   V   +D    R+L+ +G    DP  LADP V LK  +
Sbjct: 369 KNGVPIAFDCVGTMKDYVQGRKLLESGVGRIDPALLADPEVALKDLI 415


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: 391
Number of extensions: 15
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: 406
Length of database: 415
Length adjustment: 31
Effective length of query: 375
Effective length of database: 384
Effective search space:   144000
Effective search space used:   144000
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 24 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