Alignments for a candidate for sdh in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Pseudomonas simiae WCS417

Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate GFF2149 PS417_10960 quinate dehydrogenase

Query= BRENDA::Q70JN9
         (743 letters)



>FitnessBrowser__WCS417:GFF2149
          Length = 802

 Score =  473 bits (1217), Expect = e-137
 Identities = 261/665 (39%), Positives = 365/665 (54%), Gaps = 46/665 (6%)

Query: 100 SASPASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPRPGQTNKWAAETT 159
           +A  A  DWA YG+ +   R++ L +I     ++LKVA+ YHTG        N    + T
Sbjct: 159 AAGDAQKDWAHYGNTEGGSRFAALDQINRDTVNKLKVAWTYHTGDVAI-SDGNGAEDQLT 217

Query: 160 PIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTAACKGVTYFTSS----- 214
           P+++G+ +++C+  N+++ +D  TGKE+W++ +N K         C+G+ YF ++     
Sbjct: 218 PLQIGNKVFICTPHNNLIALDADTGKELWKNEVNAKSAV---WQRCRGMAYFDATAPIAQ 274

Query: 215 ------------QVPEGQPCHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLMQGLG 262
                        VP G  C  R+L  T+D RLIAVDA TG  CE FG  GQV+L  GLG
Sbjct: 275 PTQPNSSPIMPASVPAGAQCQRRLLTNTIDARLIAVDADTGKFCEDFGTHGQVDLKAGLG 334

Query: 263 ESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVNRPND 322
                +  +++ P +    VVV   V D  +   P GVIRG+D  SG+  WA+D   P D
Sbjct: 335 NVPDSYYQLSSAPLIAGTTVVVGGRVADNVQTDMPGGVIRGFDVISGQMRWAFDPGNPED 394

Query: 323 HSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSAVVAL 382
              P   + Y R TPNSWA M+ D  +  V++P G+S++D Y   R+   +K  ++V+AL
Sbjct: 395 KQAPADGSTYVRSTPNSWAPMSYDPLMNTVFLPMGSSSTDIYGVERTQLNHKYGASVLAL 454

Query: 383 DVKTGSPRWVFQTVHKDVWDYDIGSQATLMDM--PGQDGQPVPALIMPTKRGQTFVLDRR 440
           D  TG+ +WV+QTVH D+WD+D+  Q +L+D   PG D + VPA+++ TK GQ +VLDR 
Sbjct: 455 DASTGAEKWVYQTVHNDLWDFDLPMQPSLIDFTPPGSD-KAVPAVVIGTKAGQIYVLDRA 513

Query: 441 DGKPILPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDLKETDMWGMSPIDQLFCRI 500
            GKP+  V+E P  +   IP +P SPTQP S GMP +    L E+DMWG +P DQL CRI
Sbjct: 514 TGKPLTDVQEVPVKAAN-IPNEPYSPTQPKSVGMPQIGAQTLTESDMWGATPFDQLLCRI 572

Query: 501 KFRRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYDQLVTR 560
            F+   Y G +T P  DK  + +PG  GG +WGS+S DP  G +  N     ++ Q+V  
Sbjct: 573 DFKGMRYEGLYTAPGTDKS-LSFPGSLGGMNWGSISTDPVHGFIFVNDMRLGLWIQMV-- 629

Query: 561 KKADELGLMPIDDPNYKPGGGGAEGNG----AMDGTPYGIVVTPFWDQYTGMMCNRPPYG 616
                    P  +      GG A   G     + GTPY +    F     G+ C  PP+G
Sbjct: 630 ---------PSQNKAQASSGGEALNTGMGAVPLKGTPYAVNKNRFL-SVAGIPCQAPPFG 679

Query: 617 MITAIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAAAT 676
            +TAIDMK  QKV WQ P+GT    GP G+   LP +IG P  GG++ T GG++FIA   
Sbjct: 680 TLTAIDMK-TQKVAWQVPVGTVEDTGPLGIRMHLPIKIGLPTLGGTLSTQGGLIFIAGTQ 738

Query: 677 DNQIRAIDEHTGKVVWSAVLPGGGQANPMTYEA--NGHQYVAIMAGGHHFMMTPVSDQLV 734
           D  +RA +   G  VW A LP G Q  PMTY +   G QY+ I AGG     T   D ++
Sbjct: 739 DFYLRAFNSGNGDEVWKARLPVGSQGGPMTYVSPKTGKQYIVITAGGAR-QSTDRGDYVI 797

Query: 735 VYALP 739
            YALP
Sbjct: 798 AYALP 802


Lambda     K      H
   0.315    0.134    0.428 

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: 1973
Number of extensions: 116
Number of successful extensions: 10
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: 743
Length of database: 802
Length adjustment: 41
Effective length of query: 702
Effective length of database: 761
Effective search space:   534222
Effective search space used:   534222
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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