Aligments for a candidate for sdh in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for sdh in Burkholderia phytofirmans PsJN

Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate BPHYT_RS08325 BPHYT_RS08325 glucose dehydrogenase

Query= BRENDA::Q70JN9
         (743 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS08325 BPHYT_RS08325 glucose
           dehydrogenase
          Length = 837

 Score =  451 bits (1159), Expect = e-131
 Identities = 258/700 (36%), Positives = 353/700 (50%), Gaps = 72/700 (10%)

Query: 96  APQQSASPASG----DWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPRPGQT 151
           AP   A   SG    DW AYG      RYSPL +ITP+N   L+VA+ + TG    P   
Sbjct: 152 APASGAGAGSGIDPADWPAYGRTQEGTRYSPLQQITPENVKDLQVAWTFRTGDMKGPNDP 211

Query: 152 NKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTAACKGVTYF 211
            +   E TPIK+GD LY+CS    +  +D  TG   W+ +   K +       C+GV+Y 
Sbjct: 212 VEITDEVTPIKIGDLLYLCSPHQILFALDAKTGTLKWKFDPRLKSDPSFQHVTCRGVSYV 271

Query: 212 -------------------------------------------TSSQVPEGQP------- 221
                                                      T++  P   P       
Sbjct: 272 DLSAGATAAAPATAPASDATATAAAPASDTATAAAPASDTATATTTAAPAATPASDTTAT 331

Query: 222 CHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLMQGLGESVPGFVSMTTPPPVVNGV 281
           C  RI     D  L A+DA TG  CEGF N G ++L      +  G    T+P  + + V
Sbjct: 332 CTRRIYLPVNDGHLYALDALTGQRCEGFANHGDLDLQHAQPVTTAGMYEPTSPSIITSKV 391

Query: 282 VVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVNRPNDHSQPTGNNHYSRGTPNSWA 341
           ++V   V D      PSGVIRG+D  +G+ LWA+D    + +  P    HY+  +PNSWA
Sbjct: 392 IIVAGSVEDNFSNREPSGVIRGFDVRTGELLWAFDPGAKDPNHIPGAGEHYTWNSPNSWA 451

Query: 342 AMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSAVVALDVKTGSPRWVFQTVHKDVW 401
               D  L +VY+P G +  D +   R+PE+ + +S ++AL+  TG   W +QT H D+W
Sbjct: 452 PAAYDAKLDIVYLPMGVTTPDIWGGNRTPEQERYASGLLALNASTGKLAWFYQTAHHDLW 511

Query: 402 DYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTFVLDRRDGKPILPVEERPAPSPGVIPG 461
           D D  SQ TL D+ G+DGQ VP +  P K G  FVLDRR G P++P  E P P  G  PG
Sbjct: 512 DMDQPSQPTLADITGKDGQSVPVVYAPAKTGNLFVLDRRTGVPVVPAPETPVPQ-GAAPG 570

Query: 462 DPRSPTQPWS--TGMPALRVPDLKETDMWGMSPIDQLFCRIKFRRANYTGEFTPPSVDKP 519
           D  SPTQP+S  T  P+ ++ D    DMWG +  DQL CR+ F +  Y G FTPPS+   
Sbjct: 571 DHVSPTQPFSQLTYRPSKKLTD---ADMWGATMYDQLVCRVMFHKLRYEGTFTPPSLQGT 627

Query: 520 WIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYDQLVTRKKADELGLMPIDDPNYKPG 579
            + +PG  G  +WG ++ D    I +AN    P   +L+ R   +     P++      G
Sbjct: 628 LV-FPGNLGMFEWGGIAVDTDRQIAVANPIALPFVSRLIPRGPGN-----PLEPVPGAKG 681

Query: 580 GGGAEGNGAMDGTPYGIVVTPFWDQYTGMMCNRPPYGMITAIDMKHGQKVLWQHPLGTAR 639
            G   G     G PYG+V+  F   + G+ C +P +G I+AID+K  + ++W+  +GT R
Sbjct: 682 SGTESGIQPQYGVPYGVVINAFLSPF-GLPCKQPAWGYISAIDLKTNE-IVWKKRIGTVR 739

Query: 640 ANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAAATDNQIRAIDEHTGKVVWSAVLPGG 699
            + P  +P  LP+ +G P  GG +VTAGGV FI A  DN IR  D + GK VW A LP G
Sbjct: 740 DSSP--IP--LPFRMGMPMLGGPIVTAGGVAFIGATADNYIRGFDVNNGKQVWEARLPAG 795

Query: 700 GQANPMTYEANGHQYVAIMAGGHHFMMTPVSDQLVVYALP 739
           GQA PM+Y  NG QY+ I AGGH    T + D ++ YALP
Sbjct: 796 GQATPMSYSINGRQYLVIAAGGHGSFGTKLGDYVIAYALP 835


Lambda     K      H
   0.315    0.134    0.428 

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: 2179
Number of extensions: 164
Number of successful extensions: 13
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 5
Number of HSP's successfully gapped: 2
Length of query: 743
Length of database: 837
Length adjustment: 41
Effective length of query: 702
Effective length of database: 796
Effective search space:   558792
Effective search space used:   558792
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources