GapMind for catabolism of small carbon sources

 

Alignments for a candidate for andAa in Pseudomonas fluorescens FW300-N1B4

Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate Pf1N1B4_4393 Ferredoxin reductase

Query= SwissProt::Q84BZ0
         (406 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4393
          Length = 413

 Score =  240 bits (613), Expect = 5e-68
 Identities = 162/406 (39%), Positives = 210/406 (51%), Gaps = 5/406 (1%)

Query: 5   PFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVR 64
           P VIVGAGHA  R A  LR       +++IG E   PY+RP LSK  L          + 
Sbjct: 7   PLVIVGAGHAGGRAALTLRGEGYSGRLILIGDESHAPYERPPLSKGLLQGTVELAGYSLC 66

Query: 65  DAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGV 124
           D A      I    G  V  ++ +  R++L DG+ L YA+L+LATG R R      +  +
Sbjct: 67  DTAQLAELGIEHLAGNPVKCLDPQQHRLQLADGSWLHYARLLLATGGRSRRLASVPEHLL 126

Query: 125 VAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRA 184
              Y+RT  +A ALRA L    RV ++GGGFIGLEVAA AR LGC VT+++   RL  R 
Sbjct: 127 NVLYLRTHDEALALRASLQPDTRVVIIGGGFIGLEVAATARALGCTVTLLEAGPRLAGRV 186

Query: 185 LPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLPN 244
           LPE + +    LH  RGV  ++     A++      ++   D   +  D+VVVGIG+ PN
Sbjct: 187 LPEQLSSVLLELHRSRGVDVRLNVAIEAVQGTTHVESVQLVDGELLPCDLVVVGIGMQPN 246

Query: 245 VELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQPAV 304
            ELA AAGL+V  GIRVDA  RT+   IFAAG+V        G   R E+W+ AE Q   
Sbjct: 247 TELAAAAGLEVGQGIRVDAQLRTSAPDIFAAGDVCEFRLHPQGVFQRQETWRNAETQGRH 306

Query: 305 AAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLGGDGR 364
           AA NLLG +  +  +P  WSDQYD  LQ +G+    Q T  R  P  G F +F L  +  
Sbjct: 307 AALNLLGGELPFEVIPGFWSDQYDWGLQTVGVIANTQPTASRTTPG-GGFLLFYLDAEQC 365

Query: 365 IVAAAAVNLG----RDIGAARRLIAAGAMPDPQQLADPTVGLKTFL 406
           +  A     G    +DI    RLIA   +     LAD  V LK  L
Sbjct: 366 LQGACGWGQGNSIAKDIKLCERLIAHRNLLSVDALADADVPLKQLL 411


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: 342
Number of extensions: 18
Number of successful extensions: 3
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: 413
Length adjustment: 31
Effective length of query: 375
Effective length of database: 382
Effective search space:   143250
Effective search space used:   143250
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