GapMind for catabolism of small carbon sources

 

Aligments for a candidate for amaA in Burkholderia phytofirmans PsJN

Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate BPHYT_RS13575 BPHYT_RS13575 FAD-dependent oxidoreductase

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



>lcl|FitnessBrowser__BFirm:BPHYT_RS13575 BPHYT_RS13575 FAD-dependent
           oxidoreductase
          Length = 430

 Score =  250 bits (639), Expect = 5e-71
 Identities = 147/413 (35%), Positives = 215/413 (52%), Gaps = 6/413 (1%)

Query: 13  LWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSG 72
           LW   ++P V    L      DV ++G G TGLS A+HL EQG  V V++A + G G SG
Sbjct: 14  LWAATAEPAVVTPPLDNSTVVDVAIVGAGYTGLSTALHLAEQGLRVCVIDANEPGWGASG 73

Query: 73  RNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLH 132
           RN G V  G    PD++    G + G+ L ++ G A   VF ++ R GI C A   G + 
Sbjct: 74  RNGGQVIPGLKYDPDELIRRYGPRDGNALVQMAGGAADTVFDLVARHGIRCDATRAGWIQ 133

Query: 133 MAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYT 192
             H+   +  L AR  QW  RGA VELL  AQ  +  GTD      +DRRAG++ P+ Y 
Sbjct: 134 PTHSHKLLKTLYARAGQWEARGAPVELLDRAQVSKRLGTDAFVGGWVDRRAGSVQPLSYA 193

Query: 193 QGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARG-AVRAEKVVISTGAYTEGDWSNL 251
           +GLA A    G +I   +   G+ER  +GWR++TA G  + +++V+++T  YT+G W  L
Sbjct: 194 RGLARAAQAAGAQIHGGTRAAGIERGANGWRIRTAHGPVIESKQVLLATNGYTDGLWPRL 253

Query: 252 QKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDN 311
            +       + VA+KPL       +L  G+ + D+R +L   R+D  GRLL+G  GR   
Sbjct: 254 AQSVIAANSFIVATKPLADDVGATILAGGEVASDSRRLLLYFRKDADGRLLMG--GRGPF 311

Query: 312 KPAWFVRSWA--DRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYN 369
           +       WA  +R     +P+L   E+E  W G I  T + L  +  PA G+    GYN
Sbjct: 312 REPRNAADWAHLERAAQLMFPQLRGTEYEFRWAGRIAITRNFLPHVHMPAKGMTIALGYN 371

Query: 370 GRGNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLY 422
           GRG    T +G+  A + L G A  LP+P +P+  V   +L+  +  +G + Y
Sbjct: 372 GRGIAMATTLGKHLAAY-LGGAAKGLPLPPTPIEPVPLHALQRFYISAGVAWY 423


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: 492
Number of extensions: 19
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: 432
Length of database: 430
Length adjustment: 32
Effective length of query: 400
Effective length of database: 398
Effective search space:   159200
Effective search space used:   159200
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 (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 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