Alignments for a candidate for gdh in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Pseudomonas simiae WCS417

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate GFF2149 PS417_10960 quinate dehydrogenase

Query= CharProtDB::CH_002195
         (796 letters)



>FitnessBrowser__WCS417:GFF2149
          Length = 802

 Score =  592 bits (1526), Expect = e-173
 Identities = 328/809 (40%), Positives = 462/809 (57%), Gaps = 38/809 (4%)

Query: 7   GSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALW 66
           G  RLL+    +  AL GL L IGG  LV++GGSWY+ I G +M     ++   K A  W
Sbjct: 9   GVSRLLLLGLGVIIALLGLALAIGGVKLVSLGGSWYFLIGGAIMAIAGLLIACRKPAGAW 68

Query: 67  LYAALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVI-PASGAVAALV 125
           ++AA L+GT IW V +VG  FW L  R  + +F  I +++  V+  LV  PA GA A   
Sbjct: 69  VFAAFLIGTAIWAVADVGLVFWPLFSR--LFMFAAIGMVVALVYPLLVNKPARGAYA--- 123

Query: 126 VALLISGGILTWAGFNDPQEINGTLSADATPAEAISPVA----DQDWPAYGRNQEGQRFS 181
           VA +++ G+   AG      +     A       I+PVA     +DW  YG  + G RF+
Sbjct: 124 VAAVLAAGVAVAAG---NMFVAHPSVAPTGAGPGITPVAAGDAQKDWAHYGNTEGGSRFA 180

Query: 182 PLKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDA 241
            L QIN D V+ LK AW + TGDV   +  G   +++TP+++G+ +++CT H  L ALDA
Sbjct: 181 ALDQINRDTVNKLKVAWTYHTGDVAISDGNGA-EDQLTPLQIGNKVFICTPHNNLIALDA 239

Query: 242 ASGKEKWHYDPELKTNESFQHVTCRGVSYHEAKAETASPE-------------VMADCPR 288
            +GKE W  +   K   S     CRG++Y +A A  A P                A C R
Sbjct: 240 DTGKELWKNEVNAK---SAVWQRCRGMAYFDATAPIAQPTQPNSSPIMPASVPAGAQCQR 296

Query: 289 RIILPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVM 348
           R++    D RLIA++A+ GK CE F   G ++L++ + +     Y+ +S P+I   T+V+
Sbjct: 297 RLLTNTIDARLIAVDADTGKFCEDFGTHGQVDLKAGLGNVPDSYYQLSSAPLIAGTTVVV 356

Query: 349 AGSVTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAA 408
            G V DN  T    GVIRGFDV +G++ WAFDPG  +    P+D  T+  ++PNSWAP +
Sbjct: 357 GGRVADNVQTDMPGGVIRGFDVISGQMRWAFDPGNPEDKQAPADGSTYVRSTPNSWAPMS 416

Query: 409 YDAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMD 468
           YD  ++ V+LPMG ++ DI+G  RT    +Y +S+LAL+A+TG   W YQTVH+DLWD D
Sbjct: 417 YDPLMNTVFLPMGSSSTDIYGVERTQLNHKYGASVLALDASTGAEKWVYQTVHNDLWDFD 476

Query: 469 LPAQPTLADITVNG--QKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYV 526
           LP QP+L D T  G  + VP +    K G I+VLDR  G+ +    E PV       +  
Sbjct: 477 LPMQPSLIDFTPPGSDKAVPAVVIGTKAGQIYVLDRATGKPLTDVQEVPVKAANIPNEPY 536

Query: 527 TPTQPFS-ELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPG 585
           +PTQP S  +     + L+ +DMWGAT FDQL+CR+ F  MRYEG++T P    +L FPG
Sbjct: 537 SPTQPKSVGMPQIGAQTLTESDMWGATPFDQLLCRIDFKGMRYEGLYTAPGTDKSLSFPG 596

Query: 586 NLGMFEWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQY 645
           +LG   WG IS DP       N M L    +++P    N  +     +   T  G  P  
Sbjct: 597 SLGGMNWGSISTDPVHGFIFVNDMRLGLWIQMVP--SQNKAQASSGGEALNTGMGAVPLK 654

Query: 646 GVPYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPF 705
           G PY V  N FLS  G+PC+ P +G ++A+D+KT +V W+  +GT +D+ P  + + +P 
Sbjct: 655 GTPYAVNKNRFLSVAGIPCQAPPFGTLTAIDMKTQKVAWQVPVGTVEDTGPLGIRMHLPI 714

Query: 706 NMGMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTY--EVN 763
            +G+P LGG +ST G ++FIA T D YLRA+N  NG+++W+ RLP G Q  PMTY     
Sbjct: 715 KIGLPTLGGTLSTQGGLIFIAGTQDFYLRAFNSGNGDEVWKARLPVGSQGGPMTYVSPKT 774

Query: 764 GKQYVVISAGGHGSFGTKMGDYIVAYALP 792
           GKQY+VI+AGG     T  GDY++AYALP
Sbjct: 775 GKQYIVITAGG-ARQSTDRGDYVIAYALP 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: 2135
Number of extensions: 145
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: 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 Apr 09 2024. 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:

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 2024 update 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