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

GapMind for catabolism of small carbon sources

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

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate AO356_30385 AO356_30385 quinoprotein glucose dehydrogenase

Query= BRENDA::D4P700
         (796 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_30385
          Length = 811

 Score =  536 bits (1382), Expect = e-156
 Identities = 323/807 (40%), Positives = 434/807 (53%), Gaps = 39/807 (4%)

Query: 12  RFLTVLFAV---LTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYA 68
           R++  +FA+   + G  + IGGI L    GS YY+I G A + +A LLWR ++  + VYA
Sbjct: 22  RWVCRIFAIVLLMLGLALSIGGIILVADAGSAYYLITGLAFITSAVLLWRGDARGIWVYA 81

Query: 69  LLLLATLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGLYQPGKGALG----AMG 124
            +L+ T AW +WEVG + W LAPR     + G  L+LP   R    P    L     +  
Sbjct: 82  AMLVWTTAWSLWEVGFNGWQLAPRLIGPFVLGAVLLLPHFTRLKPAPSTRKLPRGWPSFA 141

Query: 125 VALVASAAVLTYSVFNDPQVVNGAL--PATADNAPQA--QPLSNIADGDWPAYARDQQGT 180
             LVA+ A+ + S    P   +  +        AP    QPL+N    DW AY  DQ GT
Sbjct: 142 GGLVAAIALGSVSHAFGPDAPDFPMLRRGVQSQAPAKLPQPLANNERTDWQAYGNDQGGT 201

Query: 181 RFSPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFA 240
           RFSPL  I+  NV +L   W+    DM  P +      E TPI +  +LY C  +  + A
Sbjct: 202 RFSPLADIDTTNVSKLVKVWE---ADMA-PVNGDLNAIEGTPIMMGSSLYACDGNNGIHA 257

Query: 241 LDAATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPALCSRRIYLPVNDG 300
            DA TGK+ W+ D  +          CRGV+Y++ P A          CS RIY P ++ 
Sbjct: 258 FDAETGKELWRRD--ISNGVPQSGKPCRGVAYYKVPDAN-------GFCSERIYAPSHNP 308

Query: 301 RLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVTDNFS 360
            L ALDA+TGE CP FGNNG +DL         G++  +S P +    IV+ G + D   
Sbjct: 309 TLVALDAKTGEYCPGFGNNGAVDLTKGVAPYPHGLFYVSSAPQVIRGKIVVGGGIPDGQY 368

Query: 361 TREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDIVY 420
              PSG IR FD  TG+L W FD GA +   +P +   +T ++PNSWAP   D KL +VY
Sbjct: 369 WGGPSGVIRAFDAVTGELAWAFDAGAPNRLGLPPEGQYYTPSTPNSWAPISADEKLGLVY 428

Query: 421 LPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTLAD 480
           LP+G  TPD +GG R P  E  +S+V+AL+A TG+L W +Q  HHD+WD D+ SQPTL +
Sbjct: 429 LPVGNATPDAYGGQRRPYDEDISSAVIALDAETGRLRWKFQATHHDIWDYDVASQPTLLN 488

Query: 481 ITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQ-GAAKGDHVSATQPYS-E 538
                G   P +  P K G IFVLDR TG+ +    E PVPQ   AKG+ +S TQP S E
Sbjct: 489 WPTAKGMR-PALIQPTKRGEIFVLDRETGEPIKAVEEQPVPQRDIAKGEWLSPTQPASVE 547

Query: 539 LTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPS-EQGTLVFPGNLGMFEWG 597
           L       L +KDMWGAT  DQ+VCR++FK+ RYEG FTP + ++  L+ PG++G   W 
Sbjct: 548 LPAFRGPQLREKDMWGATPIDQMVCRIMFKQSRYEGQFTPITLDKNVLIDPGSMGGVNWN 607

Query: 598 GISVDPHRQIAIANPMALPFVSKLIPRGPGNPE--EPPKGATGGSGTETGIQPQYGVPYG 655
           GIS+D  R + I N   +P   +L+ R            G   G   E   QP    PYG
Sbjct: 608 GISLDVDRGLMIVNWTQVPDRIELVTREEATQRNFRIAPGLDAGGQAE---QPMLDTPYG 664

Query: 656 VELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLP----FKMGMP 711
                FLS  G+PC  P WG + AVDL + +++W +  G+ RD  P  LP      +G P
Sbjct: 665 AYRVNFLSQLGIPCNAPPWGLIGAVDLVSGKLIWSKPFGSPRDIGPFGLPTLVSIPIGTP 724

Query: 712 MLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTYE--VNGKQYV 769
             GG V T G + FIG  A++  RA    TG  LW +RL     ATPMTY   V+G+Q+V
Sbjct: 725 TAGGAVTTRGGLVFIGGAAEHTFRALDAATGRELWSSRLATSANATPMTYRSPVSGRQFV 784

Query: 770 VIAAGGHGSFGTKLGDYVIAYALPDQK 796
           V+A GG   + TK G  ++A+A+PD K
Sbjct: 785 VVAEGGRPHYRTKPGSKLVAFAIPDSK 811


Lambda     K      H
   0.319    0.137    0.433 

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: 156
Number of successful extensions: 22
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: 811
Length adjustment: 41
Effective length of query: 755
Effective length of database: 770
Effective search space:   581350
Effective search space used:   581350
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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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, 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