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_011912179.1 PST_RS05065 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= CharProtDB::CH_002195
         (796 letters)



>NCBI__GCF_000013785.1:WP_011912179.1
          Length = 796

 Score =  778 bits (2008), Expect = 0.0
 Identities = 383/802 (47%), Positives = 523/802 (65%), Gaps = 26/802 (3%)

Query: 7   GSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALW 66
           G+R L +TLTAL   + G  + IGGG+L  +GGSWYY +AG+ +L VA +L+  +RAA+W
Sbjct: 6   GARPLRITLTALVILVLGALMTIGGGYLATLGGSWYYLVAGVGLLVVAGLLFTRRRAAIW 65

Query: 67  LYAALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLV---IPASGAVAA 123
           LYA LLLGT+ W  +EV FD+W L PR D+    G+WLILPFV R +    I   GA   
Sbjct: 66  LYATLLLGTLAWTFYEVRFDWWQLAPRIDLWCILGLWLILPFVNRHVSDRQIWRDGASGL 125

Query: 124 LVVALLISGGILTWAGFNDPQEINGTLSADATPAEAISPVAD-----QDWPAYGRNQEGQ 178
           L + LL    +  ++   D   I G  S DA   + ++P         +W AYG +  G 
Sbjct: 126 LGIGLLAGALMAGYSLTQDYHSITGEFS-DAQ-MQGLAPEGQAGRRASEWTAYGGSDRGD 183

Query: 179 RFSPLKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFA 238
           R++P   I   NV  LK+AW F TGD+    DPGEIT +VTP+KVGD L++CT H    A
Sbjct: 184 RYAPADLITPANVGKLKKAWEFHTGDLPGEGDPGEITYQVTPLKVGDNLFICTPHSIAIA 243

Query: 239 LDAASGKEKWHYDPELKTN-ESFQHVTCRGVSYHEAKAETASP----EVMADCPRRIILP 293
           +DA +G+E+W +DP +  + E +QH+TCRG++YH+A A   +P    +  A C RR+ LP
Sbjct: 244 VDADTGEERWRFDPSINRDAEYYQHMTCRGLAYHDATAYGQAPASPAQPAARCERRLFLP 303

Query: 294 VNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGSVT 353
            NDG LIA++  +GK CE F + G ++L++ + +   G+Y PTSPP++T+K +++ GS+T
Sbjct: 304 TNDGTLIALDVADGKPCEDFGDAGTVDLKAGLGEGALGVYLPTSPPVVTEKLVIVGGSIT 363

Query: 354 DNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAKL 413
           DN +     GVIR +DV +GEL+W FDPG  D     +   T+  ++PNSW  A  D  L
Sbjct: 364 DNGAVDSPGGVIRAYDVRSGELVWNFDPGNPDATEPLAPGETYVRSTPNSWTIATADESL 423

Query: 414 DLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPAQP 473
            LVY+P G  TPD W   RTPE ER+  +++AL+  +G++ W +QTVHHDLWD DLP+QP
Sbjct: 424 GLVYIPTGNQTPDQWAQPRTPESERFTDTLVALDLASGQVRWEFQTVHHDLWDRDLPSQP 483

Query: 474 TLADITVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPTQPFS 533
           TL DI      VP I  P K G++++LDRR GE +VP  E PVPQG   G++  PTQP+S
Sbjct: 484 TLVDIDGPQGTVPAIIQPTKRGDLYILDRRTGEPIVPVDEMPVPQGTDYGEFTAPTQPYS 543

Query: 534 ELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGMFEWG 593
            +S+ P + L   DMWG T  DQ++CR+ F Q+RYEG FTPPSEQG+L++PGN+G F W 
Sbjct: 544 AVSYAPDEPLRERDMWGGTPLDQMMCRIQFRQLRYEGDFTPPSEQGSLIYPGNVGTFNWP 603

Query: 594 GISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGVPYGVTL 653
            ++VDP+R++    P  L FVS ++ R   +P E     +  G E+G+QP  G PY V L
Sbjct: 604 SVAVDPSRQLLFGAPNYLAFVSTMVNRDDVDPEE-----RTGGGETGLQPNLGAPYMVRL 658

Query: 654 NPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMPMLG 713
            PFLS  GLPC+ P WGY++ALDL++ + VW  + GT +DS P  +P+PV    G P LG
Sbjct: 659 EPFLSVLGLPCQTPPWGYVTALDLRSMKKVWMHKNGTSRDSAPLGIPLPV----GTPALG 714

Query: 714 GPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTY--EVNGKQYVVIS 771
           GPI TAG V F++ T D YLRAY++ NG++LW+GRLPAGGQATPMTY  E  GKQYVV  
Sbjct: 715 GPIVTAGGVAFMSGTLDYYLRAYDLQNGKELWKGRLPAGGQATPMTYVSEKTGKQYVVQM 774

Query: 772 AGGHGSFGTKMGDYIVAYALPD 793
           AGGHGSFGTK+GD ++A+ L +
Sbjct: 775 AGGHGSFGTKLGDSLIAWTLDE 796


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: 2369
Number of extensions: 157
Number of successful extensions: 16
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: 796
Length adjustment: 41
Effective length of query: 755
Effective length of database: 755
Effective search space:   570025
Effective search space used:   570025
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.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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 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