Alignments for a candidate for sdh in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Paraburkholderia bryophila 376MFSha3.1

Align Glycerol dehydrogenase large subunit; EC 1.1.99.22; D-arabitol dehydrogenase large subunit; ARDH; D-sorbitol dehydrogenase subunit SldA; SLDH; Gluconate/polyol dehydrogenase large subunit (uncharacterized)
to candidate H281DRAFT_03298 H281DRAFT_03298 quinoprotein glucose dehydrogenase

Query= curated2:Q8KIL1
         (740 letters)



>FitnessBrowser__Burk376:H281DRAFT_03298
          Length = 879

 Score =  400 bits (1028), Expect = e-115
 Identities = 210/519 (40%), Positives = 295/519 (56%), Gaps = 20/519 (3%)

Query: 218 CHNRLIEGTLDMRLIAVDAETGDFCPNFGHGGQVNLMQGLGESVPGFVSMTAPPPVINGV 277
           C  R+   T D RLIA++A+TG  C +FG+ GQ++L   +G   PG    T+PP V   +
Sbjct: 380 CPRRIFLPTADARLIALNADTGQPCTHFGNNGQIDLRTNIGPFTPGGYYSTSPPAVTRDL 439

Query: 278 VVVNHEVLDGQRRWAPSGVIRGYDAESGKFVWAWDVNNSDDHSQPTGNRHYSRGTPNSWA 337
           V+++  V D +    PSGV R +D   G  VW WD  N D+    TGN+ Y R +PN W+
Sbjct: 440 VIISGHVTDNESTNEPSGVTRAFDVHDGHLVWNWDAGNPDETQPITGNQTYVRNSPNMWS 499

Query: 338 TMTGDNEEGLVYVPTGNSAADYYSALRSDAENKVSSAVVAIDVKTGSPRWVFQTAHKDVW 397
             + D + G+VY+P GN   D +  +R+ A  KV++ VVA+D+ TG  RW +Q  H D+W
Sbjct: 500 VFSVDEKLGMVYLPLGNQTPDQWGGMRTPASEKVAAGVVALDLATGKMRWNYQFTHHDLW 559

Query: 398 DYDIGSQATLMDMPGPDGQTVPALIMPTKRGQTFVLDRRTGKPILPVEERPAPSPGVIPG 457
           D D+G Q +L+D+  P G   PALI  TK+G  +VL+R TGKPI+P+ E P P  G   G
Sbjct: 560 DMDVGGQPSLIDLQTPSG-VQPALIASTKQGSLYVLNRETGKPIVPITEEPVPQ-GAGTG 617

Query: 458 DPRSPTQPWSVGMPALRVPDLKETDMWGMSPIDQLFCRIKFRRANYVGEFTPPSVDKPWI 517
           D  SPTQP+S      + P ++E DMWG +P DQL+CR+KF+   Y G FTPPS ++  +
Sbjct: 618 DHTSPTQPFSA--LNFKPPKVRERDMWGTNPFDQLWCRVKFKSLRYDGMFTPPS-EQGSL 674

Query: 518 EYPGYNGGSDWGSMSYDPQSGILIANWNITPMYDQLVTRKKADSLGLMPIDDPNFKPGGG 577
            +PG  G  DWG ++ DP   ILIAN +      +LV R +        I   N +  G 
Sbjct: 675 VFPGNFGVFDWGGIAVDPVRQILIANPSYMAFTSKLVPRSQ--------IPSDNGEKKGS 726

Query: 578 GAEGNGAMDGTPYGIVVTPFWDQYTGMMCNRPPYGMITAIDMKHGQKVLWQHPLGTARAN 637
              G     GTPYG  +  F     G+ C  PP+G +  +D++    ++W+H  GT R +
Sbjct: 727 ETSGIKLARGTPYGFELNAFLSP-LGIPCQAPPWGYVAGVDLRTNH-IVWEHKNGTIRDS 784

Query: 638 GPWGLPTGLPWEIGTPNNGGSVVTGGGLIFIGAATDNQIRAIDEHTGKVVWSAVLPGGGQ 697
            P  LP  +P  +G P+ GG + T GG+ F+    D  +RA D  TG  +W A LP GGQ
Sbjct: 785 AP--LP--IPMPLGVPSLGGMITTAGGVAFLSGTLDYYLRAYDVRTGDRLWQARLPAGGQ 840

Query: 698 ANPMTY-EANGHQYVAIMAGGHHFMMTPVSDQLVVYALP 735
           A PMTY ++NG QYV + AGGH  + T   D ++ Y LP
Sbjct: 841 ATPMTYADSNGKQYVLVTAGGHGSLGTKQGDYVIAYTLP 879



 Score = 97.4 bits (241), Expect = 3e-24
 Identities = 49/121 (40%), Positives = 72/121 (59%), Gaps = 5/121 (4%)

Query: 97  ANPARGDWVAYGRDDHQTRYSPLSEITPENASKLKVAFVYHTGSYPRPGQVNKWAAETTP 156
           AN    DW  YG      RYSPL++ITPENA +LKVA+ + TG  P PG   +   E TP
Sbjct: 167 ANRQAADWTDYGGSPLGQRYSPLTQITPENAGQLKVAWQFETGDKPGPGDPTETTDENTP 226

Query: 157 IKVGDGLYTCSAMNDIIKLDPATGKQIWRRNVDVKYHSIPYT----AACKGVTYFTSSVV 212
           IKVG+ L+ C+  + +I LDPA+GK++WR +  ++   + +       C+GV+Y   ++ 
Sbjct: 227 IKVGNKLFLCTPHSIVIALDPASGKELWRYDPHIQ-SPVGFKHWEHMTCRGVSYHDDAMY 285

Query: 213 P 213
           P
Sbjct: 286 P 286


Lambda     K      H
   0.315    0.135    0.430 

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: 2288
Number of extensions: 179
Number of successful extensions: 12
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 740
Length of database: 879
Length adjustment: 41
Effective length of query: 699
Effective length of database: 838
Effective search space:   585762
Effective search space used:   585762
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: 41 (21.5 bits)
S2: 56 (26.2 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:

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
the source code
instructions for running GapMind on your computer

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