Alignments for a candidate for sdh in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Pseudomonas putida KT2440

Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate PP_3569 PP_3569 quinate dehydrogenase (quinone)

Query= BRENDA::Q70JN9
         (743 letters)



>FitnessBrowser__Putida:PP_3569
          Length = 805

 Score =  482 bits (1241), Expect = e-140
 Identities = 265/670 (39%), Positives = 368/670 (54%), Gaps = 44/670 (6%)

Query: 93  PQMAPQQSASPASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPRPGQTN 152
           P M P ++      DWA YG+ +   R++ L +I   N ++LKVA+ Y TG        N
Sbjct: 157 PGMTPVETGKEQK-DWAHYGNTEGGSRFAALDQINRDNVNKLKVAWTYQTGDVAI-SDGN 214

Query: 153 KWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTAACKGVTYF- 211
               + TP+++G  +++C+  N+++ +D  TGKE+W++ IN + +       C+G+ YF 
Sbjct: 215 GAEDQLTPLQIGSKVFICTPHNNLIALDADTGKELWKNEINAQSKV---WQRCRGMAYFD 271

Query: 212 ----------------TSSQVPEGQPCHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQV 255
                           T   V  G  C  R+L  T+D RLIAVDA TG  C+GFGN GQV
Sbjct: 272 ATAAIAQPTQPNSSPITGVSVAAGANCQRRLLTNTIDGRLIAVDADTGEFCQGFGNNGQV 331

Query: 256 NLMQGLGESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAW 315
           +L  GLG+    +  +++ P +    VVV   V D  +   P GVIRG+D  +G+  WA+
Sbjct: 332 DLKAGLGDVPDSYYQLSSAPLMAGTTVVVGGRVADNVQTDMPGGVIRGFDVITGEMRWAF 391

Query: 316 DVNRPNDHSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENKV 375
           D   P D   P G+  Y R TPNSWA M+ D A+  V++P G+S++D Y   RS  ++  
Sbjct: 392 DPGNPEDRQAPQGDKTYVRSTPNSWAPMSYDPAMNTVFLPMGSSSTDIYGVERSKLDHTY 451

Query: 376 SSAVVALDVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTF 435
            ++V+ALD  TG+ +WVFQTVH D+WD+D+  Q +L+D    DGQ VPA+++ TK GQ +
Sbjct: 452 GASVLALDATTGNQKWVFQTVHNDLWDFDLPMQPSLIDFTKDDGQSVPAVVIGTKAGQIY 511

Query: 436 VLDRRDGKPILPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDLKETDMWGMSPIDQ 495
           VLDR  GKP+  V+E P   P  IP +P SPTQP S GMP +    L E+DMWG +P DQ
Sbjct: 512 VLDRATGKPLTQVDEVPV-KPSNIPNEPYSPTQPKSVGMPQIGAQTLTESDMWGATPYDQ 570

Query: 496 LFCRIKFRRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYD 555
           L CRI F++  Y G +T P  D   + +PG  GG +WGS+S DP  G +  N     ++ 
Sbjct: 571 LLCRIDFKKMRYDGLYTAPGTDLS-LSFPGSLGGMNWGSISTDPVHGFIFVNDMRLGLWI 629

Query: 556 QLVTRKKADELGLMPIDDPNYKPGGGGAEGNG----AMDGTPYGIVVTPFWDQYTGMMCN 611
           Q++           P  +      GG A   G     + GTPY +    F     G+ C 
Sbjct: 630 QMI-----------PSQNKGGAASGGEALNTGMGAVPLKGTPYAVNKNRFL-SVAGIPCQ 677

Query: 612 RPPYGMITAIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVF 671
            PP+G +TAIDMK  Q V WQ P+GT    GP G+   LP +IG P  GG++ T GG+VF
Sbjct: 678 APPFGTLTAIDMKTRQ-VAWQVPVGTVEDTGPLGIRMHLPIKIGLPTLGGTLSTQGGLVF 736

Query: 672 IAAATDNQIRAIDEHTGKVVWSAVLPGGGQANPMTYEA--NGHQYVAIMAGGHHFMMTPV 729
           IA   D  +RA D   G  +W A LP G Q  PMTY +   G QYV I AGG     T  
Sbjct: 737 IAGTQDFYLRAYDSSNGNEIWKARLPVGSQGGPMTYVSPKTGKQYVVITAGGAR-QSTDR 795

Query: 730 SDQLVVYALP 739
            D ++ YALP
Sbjct: 796 GDYVISYALP 805


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: 1997
Number of extensions: 123
Number of successful extensions: 8
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: 805
Length adjustment: 41
Effective length of query: 702
Effective length of database: 764
Effective search space:   536328
Effective search space used:   536328
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 Sep 17 2021. 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 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