GapMind for catabolism of small carbon sources

 

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

Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate H281DRAFT_06337 H281DRAFT_06337 Glycine/D-amino acid oxidase (deaminating)

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



>lcl|FitnessBrowser__Burk376:H281DRAFT_06337 H281DRAFT_06337
           Glycine/D-amino acid oxidase (deaminating)
          Length = 424

 Score =  156 bits (395), Expect = 1e-42
 Identities = 119/396 (30%), Positives = 187/396 (47%), Gaps = 12/396 (3%)

Query: 8   LRQQCLWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIG 67
           ++ +  W   + P V A     +  ADV VIG G TGLSAA+ L ++G SV V++A ++G
Sbjct: 1   MKLESYWLDTAPPFVTACEGPVDGLADVVVIGAGFTGLSAALALGKRGASVTVVDAGRVG 60

Query: 68  HGGSGRNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQH 127
            G SGRN G VN G       + A LG ++ S   +   +A   V  +I    IDC    
Sbjct: 61  GGASGRNGGQVNTGVAQDFVALAAQLGIERASACYRAFADAVDTVERLIREEQIDCDYLA 120

Query: 128 KGTLHMAHNATGIADLEARHEQWRRR-GADVELLTGAQCQEYCGTDKISAALLDRRAGTI 186
            G L +A     +A LE   +  RR    D+EL+ G + +    +D     LL R  G +
Sbjct: 121 SGKLKLASKPHHLAHLEKTADLIRRTVDTDIELIDGDRIRSEVQSDSFHGGLLQRHGGQM 180

Query: 187 NPMGYTQGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEG 246
           +   +T GLA A  R G K+++ ++V  + ++G   RV T RG VRA++V+I+TG    G
Sbjct: 181 HMGKFTVGLAEAAVRRGAKLYENAAVTSIVKDGGAHRVVTTRGEVRAKQVLIATGPSRHG 240

Query: 247 DWSNLQKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSL 306
            +   +++      + V ++PL      KVLP+ +    TR + +  R     RLL G  
Sbjct: 241 PFGWYRRRLAPVGSFIVVTEPLPPELLAKVLPNRRAYTTTRLMHNYFRVTPDSRLLFGGR 300

Query: 307 GR--VDNKPAWFVRSWADRIQSH----YYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAP 360
            R     +P+    + + RI        +P L     +  W G +D + D L    +   
Sbjct: 301 ARFTASERPS---DAKSGRILQQGLAVMFPMLSSARIDYCWGGLVDISADRLPHAGQ-HD 356

Query: 361 GLVAVTGYNGRGNTTGTVIGRAFAEFLLKGEADSLP 396
           G+    GY+G G    T +G+  A+ ++ G  D  P
Sbjct: 357 GIYFSMGYSGHGTQMSTHMGQVMAD-VMDGREDRNP 391


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: 498
Number of extensions: 21
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: 432
Length of database: 424
Length adjustment: 32
Effective length of query: 400
Effective length of database: 392
Effective search space:   156800
Effective search space used:   156800
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