GapMind for catabolism of small carbon sources

 

Aligments for a candidate for amaA in Pseudomonas fluorescens FW300-N1B4

Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate Pf1N1B4_4356 Gamma-glutamyl-putrescine oxidase (EC1.4.3.-)

Query= metacyc::G1G01-5614-MONOMER
         (432 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4356
           Gamma-glutamyl-putrescine oxidase (EC1.4.3.-)
          Length = 432

 Score =  139 bits (349), Expect = 2e-37
 Identities = 116/379 (30%), Positives = 176/379 (46%), Gaps = 13/379 (3%)

Query: 34  DVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGRNVG-LVNAGTWIRPDDV-EA 91
           DVCVIG G TGLS+A+ L E G SV VLEA K+G G SGRN G LVN  ++ R  DV E 
Sbjct: 35  DVCVIGAGYTGLSSALFLSEAGYSVTVLEAAKVGFGASGRNGGQLVN--SYSRDVDVIEE 92

Query: 92  TLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLHMAHNATGIADLEARHEQWR 151
             G K    L  ++ E    + + I+   I C     G +  A N   +  L  +   W 
Sbjct: 93  RYGDKTAEVLGSMIFEGADIIRSRIKEYDIQCD-YRPGGIFAALNKKQLNGLAEQKSSWE 151

Query: 152 RRG-ADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYTQGLAAAVTRLGGKIFQQS 210
           R G  ++ +L  A  +   G D     LLD + G I+P+    G AAA+ RLGGKI++QS
Sbjct: 152 RYGNKNLRMLDAADIKREVGCDNYVGGLLDMQGGHIHPLNLALGEAAAIIRLGGKIYEQS 211

Query: 211 SVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSN-LQKQFFRGYYYQVASKPLQ 269
           +   +   G+   V+TA+G VRA+ ++I+  AY   D  N + ++        V ++PL 
Sbjct: 212 AAVEI-TYGEPITVRTAKGVVRAKYLLIAGNAYLPQDLDNRVTRKSMPCGSQIVVTEPLS 270

Query: 270 GIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDNKPAWFVRSWADRIQSHYY 329
              A  ++ +     D   +L   R     RLL G       +    +           +
Sbjct: 271 EKVARSLIANNYCVEDCNYLLDYYRLTADNRLLYGGGVVYGAREPDDIEQLIRPKILKTF 330

Query: 330 PELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGRGNTTGTVIGRAFAEFLLK 389
           P+L  V+ +  WTG    T   + +          + GY+G G T   + G+  +E +++
Sbjct: 331 PQLKDVKIDYRWTGNFLLTMSRMPQFGRIEKNAYYMQGYSGHGVTCSHLAGKLISE-MIR 389

Query: 390 GEADSL----PIPFSPMSG 404
           G+A+       +P  PM G
Sbjct: 390 GDAERFDAFASLPHMPMLG 408


Lambda     K      H
   0.319    0.135    0.419 

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: 424
Number of extensions: 21
Number of successful extensions: 4
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: 432
Length of database: 432
Length adjustment: 32
Effective length of query: 400
Effective length of database: 400
Effective search space:   160000
Effective search space used:   160000
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 (21.7 bits)
S2: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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