Alignments for a candidate for gdh in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Pseudomonas fluorescens FW300-N1B4

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate Pf1N1B4_821 Glucose dehydrogenase, PQQ-dependent (EC 1.1.5.2)

Query= CharProtDB::CH_002195
         (796 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_821
          Length = 802

 Score =  757 bits (1955), Expect = 0.0
 Identities = 387/803 (48%), Positives = 514/803 (64%), Gaps = 30/803 (3%)

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

Query: 70  ALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGAVAALVV-AL 128
            +L  + +W +WEVG D+W L PR  +L   GI ++LP+  R L       V   V+ A 
Sbjct: 71  VVLFASTVWALWEVGLDWWQLVPRLALLFALGIVMLLPWFRRPLRTGEFNPVGTGVLSAA 130

Query: 129 LISGGILTWAG-FNDPQEINGTLSADATPAEAISPVA--DQDWPAYGRNQEGQRFSPLKQ 185
           ++  GI   A  F +P EI G L  DA P  + +  A  D DW +YGR+  G R+SPL Q
Sbjct: 131 VVIAGIAALASLFTNPGEIKGELDRDAVPGMSNTAPAMPDGDWNSYGRSAHGDRYSPLAQ 190

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

Query: 246 EKWHYDPELKTNES-----FQHVTCRGVSYHEAKAE--------TASPEVMADCPRRIIL 292
           E W +DP+L T  +     + H+TCRGV+YH+  A         TA+  V + CPRRI L
Sbjct: 251 ELWRFDPKLSTQNAANFKGWAHMTCRGVTYHDDAAYASEQSPTGTANAPVASVCPRRIFL 310

Query: 293 PVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGSV 352
           P  D RLIA+NA+ GK+CE F N G ++L +N+ +   G Y  TSPP +T   +V+ G V
Sbjct: 311 PTADTRLIALNADTGKMCEDFGNGGQVDLTTNIGEFTAGGYYSTSPPAVTKDLVVIGGHV 370

Query: 353 TDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAK 412
           TDN S  E SGVIR FDV+TG+L+W +D G  D     ++   +T NSPN W+  + D K
Sbjct: 371 TDNVSIDEPSGVIRAFDVHTGKLVWNWDSGNPDDTTPIAEGKVYTRNSPNMWSIFSVDEK 430

Query: 413 LDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPAQ 472
           L ++YLPMG  TPD +GG RTP+ E +A+ + AL+  TGK+ W +Q  HHDLWDMD+  Q
Sbjct: 431 LGMIYLPMGNQTPDQFGGARTPQSELHAAGLTALDIATGKVRWHFQFTHHDLWDMDVGGQ 490

Query: 473 PTLADI-TVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPTQP 531
           PTL D+ T +G K P + A  K G+I+VLDR NG+ +VP  E PVPQGA +GDY +PTQP
Sbjct: 491 PTLMDLKTADGVK-PAVLASTKQGSIYVLDRSNGQPIVPIKEIPVPQGAVEGDYTSPTQP 549

Query: 532 FSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGMFE 591
            S+L+F P   L   DMWG T FDQ++CR+ F  +RY+G+FTPPS QG++V+PGN G+F+
Sbjct: 550 MSDLNFVP-PTLKERDMWGVTPFDQMLCRIDFKSLRYDGMFTPPSLQGSIVYPGNFGVFD 608

Query: 592 WGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGVPYGV 651
           WGG+SVDP R++A  NP  + F SKLIP       E  K         G+QP  G PYGV
Sbjct: 609 WGGMSVDPVRQIAFVNPSYMAFKSKLIPAA-----EIAKQGPRVSETEGVQPNKGAPYGV 663

Query: 652 TLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMPM 711
            L   LSP GLPC+ PAWGY++A+DL TN+ +W  + GT +DS     PVP+P +MG+P 
Sbjct: 664 ILEALLSPMGLPCQAPAWGYVAAVDLTTNKTIWMHKNGTVRDS----SPVPIPLSMGVPS 719

Query: 712 LGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYE-VNGKQYVVI 770
           LGG  +TA  V F++ T D YLRAY++ NG++LW+GRLPAG Q TPMTY   +GKQYV++
Sbjct: 720 LGGAFTTASGVAFLSGTLDQYLRAYDVKNGKQLWEGRLPAGAQTTPMTYTGKDGKQYVLV 779

Query: 771 SAGGHGSFGTKMGDYIVAYALPD 793
            AGGHGS GTK GDY++AY L +
Sbjct: 780 VAGGHGSLGTKQGDYVIAYKLSE 802


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: 2242
Number of extensions: 151
Number of successful extensions: 15
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: 802
Length adjustment: 41
Effective length of query: 755
Effective length of database: 761
Effective search space:   574555
Effective search space used:   574555
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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