GapMind for catabolism of small carbon sources

 

Alignments 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:

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