Alignments for a candidate for gdh in Pseudomonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Pseudomonas stutzeri A1501

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate WP_003283008.1 PST_RS18630 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= CharProtDB::CH_002195
         (796 letters)



>NCBI__GCF_000013785.1:WP_003283008.1
          Length = 680

 Score =  545 bits (1403), Expect = e-159
 Identities = 284/645 (44%), Positives = 395/645 (61%), Gaps = 17/645 (2%)

Query: 157 AEAISPVADQDWPAYGRNQEGQRFSPLKQINADNVHNLKEAWVFRTGDVKQPNDPGEITN 216
           A A SP A  DW +YGR+    R+SPL+QI  DNV  L+ AWV++TGD+  P    +   
Sbjct: 31  ATAASP-APSDWTSYGRDNAATRYSPLRQITRDNVDQLEPAWVYQTGDMPPPEVDDKWAP 89

Query: 217 EVTPIKVGDTLYLCTAHQRLFALDAASGKEKWHYDPELKTNESFQHVTCRGVSYHEAKAE 276
           E TP+KVG++LYLC+A   L  LDA SG+E+W +DP++  +       CRGVSY+E    
Sbjct: 90  ENTPLKVGNSLYLCSAMNILIGLDAGSGRERWRFDPQVPIDHIPYSAACRGVSYYEVP-- 147

Query: 277 TASPEVMADCPRRIILPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPT 336
              PE    C RR+I    D RLIA++A+ G+ CE F N G +NL   M D+ PG    T
Sbjct: 148 --DPEPAQACARRVIEGTLDARLIAVDADTGQPCEDFGNSGQVNLLEGMGDSPPGYVAVT 205

Query: 337 SPPIITDKTIVMAGSVTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTF 396
           S P I    +V+   V D       SGVIRG+D  TGEL WA+D G      +P++   +
Sbjct: 206 SAPTIVRNVVVVGHQVLDGQKEDAPSGVIRGYDAETGELAWAWDMGRPGETGMPAEGEQY 265

Query: 397 TFNSPNSWAPAAYDAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWS 456
           T  +PN+W   + D +L LVY+PMG +  D + GNR   +  Y+++++AL+ T+G++AW 
Sbjct: 266 TRGTPNAWTTFSADDELGLVYVPMGNSAVDYFSGNREDYEHPYSTALVALDITSGEVAWV 325

Query: 457 YQTVHHDLWDMDLPAQPTLADITV-NGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKP 515
           +QTVH+D+WD DL +Q TLAD  +  GQ VP +  P K G+IFVLDRR GE +    E+P
Sbjct: 326 FQTVHNDVWDYDLGSQGTLADFPMGEGQSVPAVILPTKQGDIFVLDRRTGEPLTEVQERP 385

Query: 516 VPQGAAKGDYVTPTQPFS-ELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTP 574
           VP      + ++PTQPFS  +       L+  D WG +  DQL CR+ F Q  YEG++TP
Sbjct: 386 VPASKLPDEQLSPTQPFSVGMPTLAKPKLTERDAWGFSPLDQLWCRIQFLQSDYEGMYTP 445

Query: 575 PS-EQGTLVFPGNLGMFEWGGISVDPNREVAIANPMALPFVSKLIPRGPGN-----PMEQ 628
           PS E+  + +PG  G  +WGG S+DP R + +AN   LP   +LI R   +     P+ +
Sbjct: 446 PSVERPFIQYPGYNGGNDWGGGSLDPERGIFVANYTDLPMRDQLIRREEADEKGMVPLGE 505

Query: 629 PKDAKGTGTESGIQPQYGVPYGVTLNPFLSPF-GLPCKQPAWGYISALDLKTNEVVWKKR 687
           P    GT    G  PQ G PY +++ P+ +   G+PC +P +G I A+DL T EV+W K 
Sbjct: 506 P---GGTTDSGGPVPQAGSPYAISIKPWRNGLTGIPCTRPPYGGIMAIDLATREVLWDKP 562

Query: 688 IGTPQDSMPFPMPVPVPFNMGMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQG 747
           +GT +++ PF +P  +PF +G P  GG + TAG ++FIAAT D+ +RA ++  GE +WQ 
Sbjct: 563 LGTARNNGPFGIPSRLPFTIGTPNNGGSVITAGGLIFIAATTDDLIRAIDIDTGEVVWQD 622

Query: 748 RLPAGGQATPMTYEVNGKQYVVISAGGHGSFGTKMGDYIVAYALP 792
            LPAGGQATPMTYEVNG+QY+ I AGGH    TK+GDY+V Y+LP
Sbjct: 623 VLPAGGQATPMTYEVNGRQYLAIFAGGHHFMETKIGDYLVVYSLP 667


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: 1917
Number of extensions: 124
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: 796
Length of database: 680
Length adjustment: 40
Effective length of query: 756
Effective length of database: 640
Effective search space:   483840
Effective search space used:   483840
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 24 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