Aligments for a candidate for gdh in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for gdh in Pseudomonas simiae WCS417

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate GFF1045 PS417_05300 glucose dehydrogenase

Query= CharProtDB::CH_002195
         (796 letters)



>FitnessBrowser__WCS417:GFF1045
          Length = 805

 Score =  755 bits (1949), Expect = 0.0
 Identities = 386/805 (47%), Positives = 516/805 (64%), Gaps = 31/805 (3%)

Query: 10  RLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALWLYA 69
           RLL  L  +   + GL LL GG  L  +GGS YY +AG+ +     +L  ++RAAL LYA
Sbjct: 11  RLLPRLLGVLLLIMGLALLAGGIKLTMLGGSLYYLLAGIGITLTGVLLLATRRAALGLYA 70

Query: 70  ALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVI--PASGAVAALVVA 127
            +L  + +W +WEVG D+W L PR  +L   GI ++LP+  R L+   PA     AL VA
Sbjct: 71  LVLFASTVWALWEVGLDWWQLVPRLALLFALGIVMLLPWFRRPLLRGQPAPLGTGALSVA 130

Query: 128 LLISGGILTWAGFNDPQEI--NGTLSADATP--AEAISPVADQDWPAYGRNQEGQRFSPL 183
           ++++G     + F +P E+   G L  DA P  A A    A+ DW +YGR+  G R+SPL
Sbjct: 131 VVLAGATALASQFTNPGEMVKTGQLDRDAVPGMASAAPSQAEGDWNSYGRSAYGDRYSPL 190

Query: 184 KQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAAS 243
            QI  +N H L  AW +RTGD+  PNDPGE T E TP+KV   LY+CT H ++ ALD  +
Sbjct: 191 AQITPENAHKLVPAWTYRTGDIPGPNDPGETTAENTPLKVNGMLYVCTPHSQVIALDPDT 250

Query: 244 GKEKWHYDPELKTN--ESFQ---HVTCRGVSYHEAKAE--------TASPEVMAD-CPRR 289
           GKE W +DP++ +   E+F+   H+TCRGVSYH+  A         +ASP    + CP+R
Sbjct: 251 GKEIWRFDPKISSMGAENFKGWAHMTCRGVSYHDDAAYASEQSPTGSASPSAAPNACPKR 310

Query: 290 IILPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMA 349
           I +P  D RLIA+NA+ GK+CE F +KG ++L++N+    PG Y  TSPP +T   +V+ 
Sbjct: 311 IFVPTADTRLIALNADTGKMCEDFGDKGQVDLRANIGGFAPGGYYSTSPPAVTKNLVVIG 370

Query: 350 GSVTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAY 409
           G VTDN ST E SGVIR FDV+TG+L+W +D G  D     ++  T+T NSPN W+  A 
Sbjct: 371 GHVTDNVSTDEPSGVIRAFDVHTGKLVWNWDSGNPDDTTPLAEGKTYTRNSPNMWSMFAV 430

Query: 410 DAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDL 469
           D KL ++YLPMG   PD +GG+RT + E+YA+ + AL+  TG + W++Q  HHDLWDMD+
Sbjct: 431 DEKLGMLYLPMGNQMPDQYGGDRTDDSEKYAAGLTALDIDTGHVKWTFQFTHHDLWDMDV 490

Query: 470 PAQPTLADITVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPT 529
             QP+L DI         + A  K G+I+VLDR  G+ VVP  E  VPQGA  GD  +PT
Sbjct: 491 GGQPSLIDIKTEAGVKQAVMASTKQGSIYVLDRATGQPVVPIHEVAVPQGAVAGDRTSPT 550

Query: 530 QPFSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGM 589
           QP S+L+F P   L   DMWG T FDQL+CR+ F  MRY+G FTPPS QG++V+PGN G+
Sbjct: 551 QPKSDLNFMP-PPLKERDMWGVTPFDQLLCRIDFKSMRYDGAFTPPSLQGSIVYPGNFGV 609

Query: 590 FEWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGVPY 649
           F+WGGISVDP R++A  NP  + F SKLIP       +  K         G+QP  G PY
Sbjct: 610 FDWGGISVDPVRQIAFVNPSYMAFKSKLIPAA-----DIAKQGPRVSETEGVQPNKGAPY 664

Query: 650 GVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGM 709
           GV L   LSP GLPC+ PAWGY++A+DL T++ +W  + GT +DS     PVP+P  MG+
Sbjct: 665 GVILEAMLSPMGLPCQAPAWGYVAAVDLTTHKTIWMHKNGTVRDS----APVPIPLTMGV 720

Query: 710 PMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYE-VNGKQYV 768
           P LGG  +TAG V F++ T D YLRAY++ NG++LW+GRLPAG Q TPMTY   +GKQYV
Sbjct: 721 PSLGGTFTTAGGVAFLSGTLDQYLRAYDVKNGKQLWEGRLPAGAQTTPMTYTGKDGKQYV 780

Query: 769 VISAGGHGSFGTKMGDYIVAYALPD 793
           ++ AGGHGS GTK GDY++A+ LP+
Sbjct: 781 LVMAGGHGSLGTKQGDYVMAFKLPE 805


Lambda     K      H
   0.319    0.137    0.436 

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: 2240
Number of extensions: 152
Number of successful extensions: 13
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: 796
Length of database: 805
Length adjustment: 41
Effective length of query: 755
Effective length of database: 764
Effective search space:   576820
Effective search space used:   576820
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: 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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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