Alignments for a candidate for gdh in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Pseudomonas fluorescens GW456-L13

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate PfGW456L13_1173 Quinate/shikimate dehydrogenase [Pyrroloquinoline-quinone] (EC 1.1.99.25)

Query= CharProtDB::CH_002195
         (796 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1173
          Length = 784

 Score =  643 bits (1658), Expect = 0.0
 Identities = 339/798 (42%), Positives = 477/798 (59%), Gaps = 35/798 (4%)

Query: 7   GSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALW 66
           GS+ LL  L  L A L GL L  GGG+L+A+GGSWY+ + GL ML    M+ R K    W
Sbjct: 9   GSKWLLAGLGVLIA-LIGLGLAGGGGYLIALGGSWYFLLMGLAMLASGLMIARRKPLGAW 67

Query: 67  LYAALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGAVAAL-- 124
           LY   L+ T IW VW+ G ++W L  R  IL F  I L++  ++  LV  ASGA      
Sbjct: 68  LYGVALVLTAIWAVWDAGLEYWPLVSR--ILTFAVIGLVVALIYPTLV-RASGATGGRGA 124

Query: 125 --VVALLISGGILTWAGFNDPQEINGTLSADATPAEAISPVA----DQDWPAYGRNQEGQ 178
             +  +L    + T A    P  +       AT   A++PV      +DW  +G    G 
Sbjct: 125 YGLAGILGVAVVATMAYMFVPTHV-----VKATTEPAVTPVTPGTEQKDWAHWGNTTAGN 179

Query: 179 RFSPLKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFA 238
           RF+ L QIN  N+  L+ AW FRTGD+ Q    G   ++ TP+++GDT+Y CTA+ ++FA
Sbjct: 180 RFAALDQINKGNIDKLQVAWTFRTGDIPQSTGAGA-EDQNTPLQIGDTVYTCTAYGKVFA 238

Query: 239 LDAASGKEKWHYDPELKTNESFQHVTCRGVSYHEAKAETASPEVMADCPRRIILPVNDGR 298
           LDA +G ++W +DP+  T  ++Q   CRG+ Y E     +S      C +R+ LP  D R
Sbjct: 239 LDADTGAQRWKFDPQ-GTAPNWQR--CRGLGYSETPV--SSDNQPTACTKRLFLPTGDAR 293

Query: 299 LIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGSVTDNFST 358
           LIAINA+ GK CE F NKG ++L ++M + KPG Y+ TS P++    +++ G V DN+ST
Sbjct: 294 LIAINADTGKPCEEFGNKGTVDLTTDMGEVKPGYYQQTSTPLVAGDVVIVGGRVADNYST 353

Query: 359 RETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAKLDLVYL 418
            E  GV+R +DV +GEL+WA+DPG  +    P    T+T  +PN W+  +YDAKL LVYL
Sbjct: 354 GEPPGVVRAYDVRSGELVWAWDPGNPNTTKRPPAGETYTRGTPNVWSAMSYDAKLGLVYL 413

Query: 419 PMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPAQPTLADI 478
           P G  TPD +GG RT   ++++SSI+A++  TG++ W +QT HHDLWD DLPAQP L D+
Sbjct: 414 PTGNATPDFFGGQRTEFDDKWSSSIVAIDVKTGQVRWHFQTTHHDLWDFDLPAQPLLYDV 473

Query: 479 TVN-GQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPTQPFS-ELS 536
             + G   P +    K G IF+L+R  G  +    E+PVPQG   G+  +PTQPFS ++ 
Sbjct: 474 PDDKGGTQPALAQVTKQGEIFLLNRETGVPIARVEERPVPQGKVPGERYSPTQPFSVDMP 533

Query: 537 FRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGMFEWGGIS 596
               K L+ +DMWGAT FDQL+CR+ F  MR+EG++TPP     L FPG+LG   WG +S
Sbjct: 534 SIGNKTLTESDMWGATPFDQLMCRIQFKGMRHEGVYTPPGMDRALQFPGSLGGMNWGSVS 593

Query: 597 VDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGVPYGVTLNPF 656
           VDPN      N M L   + +IPR           A  +G E G+ PQ G P+G     F
Sbjct: 594 VDPNTHYMFINDMRLGLANYMIPR-------DKIGAGASGIEMGVVPQEGTPFGAMRERF 646

Query: 657 LSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMPMLGGPI 716
           LS  G+PC++P +G +SA+DLKT+++VW+  +GT QD+ P  + + +P  +GMP LG  +
Sbjct: 647 LSAVGIPCQKPPFGTMSAIDLKTHKLVWQVPVGTVQDTGPLGIRMHLPIPIGMPTLGASL 706

Query: 717 STAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTY--EVNGKQYVVISAGG 774
           +T   +LF A T D YLRA++  NG ++W+ RLP G Q+ PMTY     G+QY++++ GG
Sbjct: 707 ATQSGLLFFAGTQDFYLRAFDTGNGNEIWKSRLPVGSQSGPMTYVSPKTGRQYILLTVGG 766

Query: 775 HGSFGTKMGDYIVAYALP 792
                T  GDY++AYALP
Sbjct: 767 -ARQSTDRGDYVIAYALP 783


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: 2297
Number of extensions: 159
Number of successful extensions: 13
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 796
Length of database: 784
Length adjustment: 41
Effective length of query: 755
Effective length of database: 743
Effective search space:   560965
Effective search space used:   560965
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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Protein sequences (fasta format)
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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