GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Pseudomonas fluorescens FW300-N2C3

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate AO356_17600 AO356_17600 glucose dehydrogenase

Query= CharProtDB::CH_002195
         (796 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_17600
          Length = 804

 Score =  775 bits (2001), Expect = 0.0
 Identities = 396/810 (48%), Positives = 528/810 (65%), Gaps = 42/810 (5%)

Query: 10  RLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALWLYA 69
           RLL +L  +   L GL LL GG  L  +GGSWYY +AG+ +     +L  ++RAAL LYA
Sbjct: 11  RLLPSLLGILLLLMGLALLAGGVKLSTLGGSWYYLLAGIGLALTGVLLIMARRAALGLYA 70

Query: 70  ALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGAVA--ALVVA 127
            +L  + +W +WEVG D+W L PR  +L   GI ++LP+  R L+   + A    AL  A
Sbjct: 71  LVLFASTVWALWEVGLDWWQLVPRLAMLFALGIVMLLPWFRRPLLTADASATGTRALGAA 130

Query: 128 LLISGGILTWAGFNDPQEINGTLSADATPAEAISPVA--DQDWPAYGRNQEGQRFSPLKQ 185
           ++I+G     + F +P EI G L  DA P    +  A  D DW +YGR+  G R+SPL Q
Sbjct: 131 VVIAGVAALASQFTNPGEIKGQLDRDAVPGMTNTAPAMPDGDWNSYGRSAHGDRYSPLAQ 190

Query: 186 INADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGK 245
           I  +NV  LKEAW +RTGD+  PNDPGE T E TP+KV   LY+CT H ++ AL+  +GK
Sbjct: 191 ITPENVSKLKEAWTYRTGDLPGPNDPGETTAENTPLKVNGMLYVCTPHSQVIALEPETGK 250

Query: 246 EKWHYDPELKTNES-----FQHVTCRGVSYHE----AKAE-----TASPEVMAD-CPRRI 290
           E W +DP+L T ++     + H+TCRGV+YH+    A AE     TAS    +  CPRRI
Sbjct: 251 EIWRFDPKLSTQKAENFKGWAHMTCRGVTYHDDAVYASAEQSPTGTASTAPASTVCPRRI 310

Query: 291 ILPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAG 350
            LP  D RLIA+NA+ GK+CE F +KG ++L +N+     G Y  TSPP +T   +V+ G
Sbjct: 311 FLPTADTRLIALNADTGKMCEDFGDKGQVDLTANIGGFTAGGYYSTSPPAVTQNLVVIGG 370

Query: 351 SVTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYD 410
            VTDN ST E SGVIR +DV+TG+L+W +D G  D     ++  T+T NSPN W+  + D
Sbjct: 371 HVTDNVSTDEPSGVIRAYDVHTGKLVWNWDSGNPDDTTPIAEGQTYTRNSPNMWSMFSVD 430

Query: 411 AKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLP 470
            KL ++YLPMG  TPD +GG RTPE E+YA+ + AL+  TGK+ W +Q  HHDLWDMD+ 
Sbjct: 431 EKLGMLYLPMGNQTPDQFGGLRTPESEKYAAGLTALDIATGKVRWYFQFTHHDLWDMDVG 490

Query: 471 AQPTLADI-TVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPT 529
            QPTL ++ T +G K P + A  K G+I+VLDR NG+ +VP  E PVPQGA +GD+ +PT
Sbjct: 491 GQPTLMNMKTADGVK-PAVLASTKQGSIYVLDRSNGQPIVPIKEIPVPQGAVEGDHTSPT 549

Query: 530 QPFSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGM 589
           QP S+L+F P   L   DMWG T FDQ++CR+ F  +RY+G+FTPPS QG++V+PGN G+
Sbjct: 550 QPMSDLNFVPPV-LKERDMWGVTPFDQMLCRIDFKSLRYDGMFTPPSLQGSIVYPGNFGV 608

Query: 590 FEWGGISVDPNREVAIANPMALPFVSKLIPR-----GPGNPMEQPKDAKGTGTESGIQPQ 644
           F+WGGISVDP R++A  NP  + F SKL+P      GPG   E            G+QP 
Sbjct: 609 FDWGGISVDPVRQIAFVNPSYMAFKSKLVPAAEVAGGPGRKSE----------TEGVQPN 658

Query: 645 YGVPYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVP 704
            G PYGV L   LSP GLPC+ PAWGY++A+DL  N+ +WK + GT +DS     PVP+P
Sbjct: 659 KGAPYGVILEALLSPMGLPCQAPAWGYVAAVDLTNNKTLWKHKNGTVRDS----SPVPIP 714

Query: 705 FNMGMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYE-VN 763
            +MG+P LGG  +T   + F++ T D YLRAY++ NG++LW+GRLPAG Q TPMTY   +
Sbjct: 715 LSMGVPSLGGTFTTGSGLAFLSGTLDQYLRAYDVKNGKQLWEGRLPAGAQTTPMTYTGKD 774

Query: 764 GKQYVVISAGGHGSFGTKMGDYIVAYALPD 793
           GKQYV++ AGGHGS GTK GDY++AY LPD
Sbjct: 775 GKQYVLVVAGGHGSLGTKQGDYVIAYKLPD 804


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: 2250
Number of extensions: 146
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: 804
Length adjustment: 41
Effective length of query: 755
Effective length of database: 763
Effective search space:   576065
Effective search space used:   576065
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