GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gdh in Pseudomonas fluorescens FW300-N2E2

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate Pf6N2E2_5442 Glucose dehydrogenase, PQQ-dependent (EC 1.1.5.2)

Query= CharProtDB::CH_002195
         (796 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5442 Glucose
           dehydrogenase, PQQ-dependent (EC 1.1.5.2)
          Length = 804

 Score =  774 bits (1998), Expect = 0.0
 Identities = 393/810 (48%), Positives = 527/810 (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  LVLFASTVWALWEVGLDWWQLVPRLALLFALGIVMLLPWFRRPLLTADASATGTRALGAA 130

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

Query: 186 INADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGK 245
           I  +NV  L  AW +RTGD+  PNDPGE T E TP+K    LY+CT H ++ AL+  +GK
Sbjct: 191 ITPENVSKLVPAWTYRTGDLPGPNDPGETTAENTPLKANGMLYVCTPHSQVIALEPETGK 250

Query: 246 EKWHYDPELKTNES-----FQHVTCRGVSYHE----AKAETASPEVMAD------CPRRI 290
           E W +DP+L T ++     + H+TCRGV+YH+    A AE +   V +       CPRRI
Sbjct: 251 EIWRFDPKLSTQKAENFKGWAHMTCRGVTYHDDAVYASAEQSPTGVASTSPASTTCPRRI 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  A  ++  T+T NSPN W+  + D
Sbjct: 371 HVTDNVSTDEPSGVIRAYDVHTGKLVWNWDSGNPDDTAPIAEGKTYTRNSPNMWSMFSVD 430

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

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

Query: 530 QPFSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGM 589
           QP S+L+F P   L   DMWG T FDQ++CR+ F  +RYEG+FTPPS QG++V+PGN G+
Sbjct: 550 QPMSDLNFVPPV-LKERDMWGVTPFDQMLCRIDFKSLRYEGMFTPPSLQGSIVYPGNFGV 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  +TA  + F++ T D YLRAY++ NG++LW+GRLPAG Q TPMTY   +
Sbjct: 715 LSMGVPSLGGTFTTASGLAFLSGTLDQYLRAYDVKNGKQLWEGRLPAGAQTTPMTYTGKD 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: 2243
Number of extensions: 148
Number of successful extensions: 12
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 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