GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS13575
          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:

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