Alignments for a candidate for gdh in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Rhizorhabdus wittichii RW1

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate WP_011952861.1 SWIT_RS10225 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= CharProtDB::CH_002195
         (796 letters)



>NCBI__GCF_000016765.1:WP_011952861.1
          Length = 784

 Score =  568 bits (1465), Expect = e-166
 Identities = 317/798 (39%), Positives = 432/798 (54%), Gaps = 37/798 (4%)

Query: 7   GSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALW 66
           G RR+L    A  + L G+ + + G +L+ +GGS YY +AG++++  A  LWR +    W
Sbjct: 12  GLRRVLERAFAGISLLAGMGMALPGAYLLTLGGSAYYLVAGVLLVAAAVELWRGRARGAW 71

Query: 67  LYAALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWR------RLVIPASGA 120
           L+  + LGT+ W +WE G D WAL PR  +L   GI L L   WR      R+    + A
Sbjct: 72  LFLLVWLGTLGWALWEAGLDGWALLPRLGLLTGMGIALAL-IRWRPRRGTVRIAATGAAA 130

Query: 121 VAALV-VALLISGGILTWAGFNDPQEINGTLSADATPAEAISPVADQDWPAYGRNQEGQR 179
           +A+L  + L ++G              N +L   A+PA +    AD +W   GR     R
Sbjct: 131 IASLAGIGLALTGS-----------HGNASLPLAASPATS---AADGEWQHIGRTAGADR 176

Query: 180 FSPLKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFAL 239
           FSPL QI   N+  L+ AW    G    P      T E TP+ VGDTLY C  +  + A+
Sbjct: 177 FSPLDQITPANIGKLRVAWTAHLG---MPPKGLAGTIEATPLMVGDTLYTCNMNNAVIAI 233

Query: 240 DAASGKEKWHYDPELKTNESFQHVTCRGVSYHEAKAETASPEVMADCPRRIILPVNDGRL 299
           D  SGK +W +DP++          CRGV+YH        P     C  RI +   D RL
Sbjct: 234 DPDSGKTRWAFDPKIDP-AGVAMAVCRGVAYHR------QPGAAGPCAARIFVATLDNRL 286

Query: 300 IAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGSVTDNFSTR 359
           IA++A  G+ C  F   G ++L   M D   G Y PTSPP +    +V+ G V D     
Sbjct: 287 IALDAATGRRCRDFGRNGEVSLLDGMGDVPKGYYYPTSPPAVIRDRLVIGGRVADGQMVN 346

Query: 360 ETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAKLDLVYLP 419
           E SGVIR FD  TG L WA+D G  D + +P    T+T  +PN+W P + D +L L ++P
Sbjct: 347 EPSGVIRAFDAMTGRLAWAWDMGRPDRHGLPPAGETYTRGTPNAWPPISGDDRLGLAFVP 406

Query: 420 MGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPAQPTLADIT 479
           +G  TPD    +RTPE  RY SS++AL+  TGK  W YQT H D+WD DLPA  +L D  
Sbjct: 407 LGNPTPDYVMSHRTPEMRRYGSSVVALDVETGKERWHYQTTHLDVWDYDLPAPASLVDFP 466

Query: 480 VNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPTQPFS-ELSFR 538
                 P +  P K G  FVLDR  G+ +V   E+ VPQGAA G+ ++PTQP+   +   
Sbjct: 467 TARGLRPALIQPTKRGQFFVLDRETGKPLVETVERAVPQGAAPGESLSPTQPYPVGMPSL 526

Query: 539 PTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTP-PSEQGTLVFPGNLGMFEWGGISV 597
               LS A MWG T FDQ+ CR+ F Q RY+G FTP  +++ ++V PG  G   W GIS+
Sbjct: 527 AGPRLSEARMWGITPFDQIWCRIRFRQARYDGEFTPVGADRPSIVSPGYFGGSNWSGISI 586

Query: 598 DPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQ-PQYGVPYGVTLNPF 656
           DP R V +AN M  P  ++LI R   +P        G    SG    Q G PY V   PF
Sbjct: 587 DPERRVMVANVMHFPMYNQLIARADADPAVFQPARVGRHPISGENWAQQGTPYAVRTVPF 646

Query: 657 LSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMPMLGGPI 716
           +SP  +PC QP +  I+A+DL    V+W++ +GT +D+ P+ +   +P  +G+P LGG +
Sbjct: 647 VSPLKIPCNQPPYSEIAAVDLGRRAVLWREPLGTARDTGPWNVASHLPIRVGVPALGGTL 706

Query: 717 STAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYEV--NGKQYVVISAGG 774
            T   ++FIAAT +   RA+++ +G  LWQ RLPAGG A PMTY     G+QYVVI A G
Sbjct: 707 VTRSGLVFIAATQERAFRAFDLRSGHLLWQDRLPAGGHANPMTYRSPRTGRQYVVIPASG 766

Query: 775 HGSFGTKMGDYIVAYALP 792
           H  F     D +VAYALP
Sbjct: 767 HSRFANGSADLLVAYALP 784


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: 2127
Number of extensions: 139
Number of successful extensions: 13
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: 784
Length adjustment: 41
Effective length of query: 755
Effective length of database: 743
Effective search space:   560965
Effective search space used:   560965
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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 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