Aligments for a candidate for sdh in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Aligments for a candidate for sdh in Pseudomonas fluorescens FW300-N2E3

Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate AO353_16045 AO353_16045 glucose dehydrogenase

Query= BRENDA::Q70JN9
         (743 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_16045
          Length = 803

 Score =  463 bits (1192), Expect = e-134
 Identities = 262/668 (39%), Positives = 366/668 (54%), Gaps = 45/668 (6%)

Query: 96  APQQSASPA--SGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPRPGQTNK 153
           A   S +PA   G+W AYG  +   RYSPL +ITP N  +L+ A+   TG  P      +
Sbjct: 158 ADMTSTAPAMPEGEWQAYGRTEFGDRYSPLKQITPANVGKLQEAWRIRTGDLPTADDPVE 217

Query: 154 WAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEK----YEAIPYTAACKGVT 209
              E TP+KV   LY C+A + ++ +DP TGKE+WR +   K    ++   +   C+GV+
Sbjct: 218 LTNENTPLKVNGMLYACTAHSKVLALDPDTGKELWRFDPQIKSPVGFKGFAHMT-CRGVS 276

Query: 210 YF-----------TSSQVPEG-----QPCHNRILEGTLDMRLIAVDAATGNLCEGFGNGG 253
           Y+           +S+ + E      Q C  R+   T D RLIA++A TG +CEGFG+ G
Sbjct: 277 YYDENAYAKADNASSAVISEAGKAVAQACPRRLYLPTADARLIALNADTGKVCEGFGDHG 336

Query: 254 QVNLMQGLGESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLW 313
            V+L QG+G   PG    T+P  +   +V++   V D +    PSGVIR +D   G  +W
Sbjct: 337 VVDLTQGIGPFTPGGYYATSPAAITRDLVIMGGHVTDNESTNEPSGVIRAFDIRDGHLVW 396

Query: 314 AWDVNRPNDHSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEEN 373
            WD   P           Y+R +PN W+  + D  LG+VY+P GN   D + A R+P   
Sbjct: 397 NWDSGNPEATEPLAPGKTYTRNSPNMWSLASVDEKLGMVYLPLGNQMPDQWGADRTPGAE 456

Query: 374 KVSSAVVALDVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQ 433
           K S+ +VALD+ TG  RW FQ  H D+WD D+GSQ TL+DM   DG   PALI PTK+G 
Sbjct: 457 KFSAGMVALDLATGKVRWNFQFTHHDLWDMDVGSQPTLLDMKTADGIK-PALIAPTKQGS 515

Query: 434 TFVLDRRDGKPILPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDLKETDMWGMSPI 493
            +VLDRR+G PI+P+ E PAP  G + GD  +PTQ  S     L  PDL E  MWG SP 
Sbjct: 516 LYVLDRRNGTPIVPIREVPAPQ-GAVTGDHTAPTQARSD--LNLLAPDLTEKAMWGASPF 572

Query: 494 DQLFCRIKFRRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPM 553
           DQ+ CRI+F++  Y G++TPPS+    I YPG  G  +WGSVS DP   +L  + N    
Sbjct: 573 DQMLCRIQFKQLRYEGQYTPPSLQGSLI-YPGNVGVFNWGSVSLDPVRQMLFTSPNYMAF 631

Query: 554 YDQLVTRKKADELGLMPIDDPNYKPGGGGAEGNGAMDGTPYGIVVTPFWDQYTGMMCNRP 613
             +L+ + +         +    +P            G PY + + PF   + G+ C  P
Sbjct: 632 VSKLIPQAEVAAGSKRESETSGVQPN----------TGAPYAVTMHPFMSPF-GVPCQAP 680

Query: 614 PYGMITAIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIA 673
            +G +  ID+    KV+W+   GT+R + P  LP GLP  IG P+ GGS+VTAGGV F++
Sbjct: 681 AWGYVAGIDLT-TSKVVWKRKNGTSRDSSP--LPIGLP--IGVPSMGGSIVTAGGVGFLS 735

Query: 674 AATDNQIRAIDEHTGKVVWSAVLPGGGQANPMTYEA-NGHQYVAIMAGGHHFMMTPVSDQ 732
              D  +RA D + GK +W + LP GGQA PMTY   +G QYV ++ GGH  + T + D 
Sbjct: 736 GTLDQYLRAYDVNNGKELWKSRLPAGGQATPMTYTGKDGKQYVLLVVGGHGSLGTKMGDY 795

Query: 733 LVVYALPD 740
           ++ Y L +
Sbjct: 796 VIAYKLSE 803


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: 2025
Number of extensions: 142
Number of successful extensions: 11
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: 803
Length adjustment: 41
Effective length of query: 702
Effective length of database: 762
Effective search space:   534924
Effective search space used:   534924
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, 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