GapMind for catabolism of small carbon sources

 

Alignments for a candidate for andAa in Marinobacter adhaerens HP15

Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate GFF3407 HP15_3349 FAD-dependent pyridine nucleotide-disulfide oxidoreductase

Query= SwissProt::Q84BZ0
         (406 letters)



>FitnessBrowser__Marino:GFF3407
          Length = 384

 Score =  125 bits (315), Expect = 2e-33
 Identities = 84/273 (30%), Positives = 131/273 (47%), Gaps = 1/273 (0%)

Query: 5   PFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVR 64
           P +IVG G +    A  +R +D + P++++ A+  + Y +P LS       D +  A   
Sbjct: 6   PIIIVGTGLSGYSLAREIRKQDKETPVLIVTADDGVSYSKPMLSTGFTKGKDADGLAQGG 65

Query: 65  DAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGV 124
             A  D   + +R    V  I+ EA  + L D   L Y+KLVLA G+ V   G   D   
Sbjct: 66  TDAMADQLNVRIRTFVTVTGIDTEAHELILGD-ERLAYSKLVLAWGADVIRLGLDGDGQE 124

Query: 125 VAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRA 184
               +  + D RA R  L  G+RVA++G G IG E A   R  G  V VI P+  ++   
Sbjct: 125 HVFSINDLMDYRAFRDALGDGKRVAIMGAGLIGCEFANDLRNGGYEVDVIAPSEEVMPGL 184

Query: 185 LPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLPN 244
           LPE       +  +  GVGF + T+   I     G ++   +   + AD+V+  +G+ P 
Sbjct: 185 LPEAAAHAVQQELENLGVGFHLGTVVDRIDRRGDGVSLTLANGETLDADLVLSAVGLRPR 244

Query: 245 VELAQAAGLDVDNGIRVDAGCRTADRAIFAAGE 277
            +LA+AAGL+   GI V+    T+   ++A G+
Sbjct: 245 TDLARAAGLETARGIVVNRALETSAPDVYALGD 277


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: 297
Number of extensions: 17
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: 384
Length adjustment: 31
Effective length of query: 375
Effective length of database: 353
Effective search space:   132375
Effective search space used:   132375
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