GapMind for catabolism of small carbon sources

 

Aligments for a candidate for andAa in Paraburkholderia bryophila 376MFSha3.1

Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate H281DRAFT_03846 H281DRAFT_03846 3-phenylpropionate/trans-cinnamate dioxygenase ferredoxin reductase subunit

Query= SwissProt::Q84BZ0
         (406 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_03846 H281DRAFT_03846
           3-phenylpropionate/trans-cinnamate dioxygenase
           ferredoxin reductase subunit
          Length = 419

 Score =  254 bits (650), Expect = 3e-72
 Identities = 159/402 (39%), Positives = 210/402 (52%), Gaps = 4/402 (0%)

Query: 7   VIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDA 66
           VIVGA +A  + A + R    D  IV+IG E   PY RP LSK  L     E+R  +R  
Sbjct: 6   VIVGASYAGLQLAASARESGHDGDIVLIGDEPHAPYQRPPLSKGFLTGSFAEERLPLRSP 65

Query: 67  AWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGVVA 126
           A+Y   R+     TR   I+RE +++ L DG  L Y  L L TG+RVR       +    
Sbjct: 66  AFYGEMRMQWMPSTRALRIDRERKQIELHDGARLAYDHLALTTGARVRKLDCKGASHDAV 125

Query: 127 HYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRALP 186
           HY+R + DAR L  +    RR  V+GGG+IGLE AA+ RQ G +VTV++  AR+L R   
Sbjct: 126 HYLRDLRDARRLVERTQTARRAVVVGGGYIGLEAAASLRQKGLDVTVVETEARVLARVAS 185

Query: 187 EVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLPNVE 246
             +     R H   GV   +     AI   A G A+   D   +  D+VVVGIGVLPN E
Sbjct: 186 PSISVIMQRAHTRHGVSLALGRKVVAIHDVADGVAVELDDGARLSCDLVVVGIGVLPNTE 245

Query: 247 LAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTM---HFNPLLGRHVRIESWQVAENQPA 303
           LA   GLDV  GI VDA  RT+D +I AAG+      ++ P      RIES Q A +   
Sbjct: 246 LAAGCGLDVAGGIVVDACARTSDPSIVAAGDCAAFVPYWAPTGSAACRIESVQNANDMAR 305

Query: 304 VAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLGGDG 363
            AAA++LG  + Y  +PW WSDQYD  LQM G+        VRG    G F++F    D 
Sbjct: 306 TAAASVLGRSEPYRAVPWFWSDQYDLKLQMAGVNTGFTDFAVRGSVDEGKFSLFYF-RDD 364

Query: 364 RIVAAAAVNLGRDIGAARRLIAAGAMPDPQQLADPTVGLKTF 405
           R+VA  ++N  +D   AR+L++ G     + +  P   LK F
Sbjct: 365 RLVAVDSINRPQDHMLARKLLSTGTRLSVEDVNGPGFDLKAF 406



 Score = 25.8 bits (55), Expect = 0.003
 Identities = 9/22 (40%), Positives = 17/22 (77%)

Query: 147 RVAVLGGGFIGLEVAAAARQLG 168
           R+ ++G  + GL++AA+AR+ G
Sbjct: 4   RLVIVGASYAGLQLAASARESG 25


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: 376
Number of extensions: 20
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 406
Length of database: 419
Length adjustment: 31
Effective length of query: 375
Effective length of database: 388
Effective search space:   145500
Effective search space used:   145500
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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