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_011952799.1 SWIT_RS09910 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= CharProtDB::CH_002195
         (796 letters)



>NCBI__GCF_000016765.1:WP_011952799.1
          Length = 783

 Score =  558 bits (1437), Expect = e-163
 Identities = 306/792 (38%), Positives = 427/792 (53%), Gaps = 23/792 (2%)

Query: 7   GSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALW 66
           G+RR+L    A  + L G+ + + G +L+ +GGS YY +AG++++  A  LWR +    W
Sbjct: 10  GARRMLERAFAGISLLAGMGMALPGAYLLTLGGSTYYLVAGVLLVAAAVDLWRGRARGAW 69

Query: 67  LYAALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGAVAALVV 126
           L+  + LGT+ W +WE G D WAL PR  +L   GI L L   WR     A  A  A   
Sbjct: 70  LFLLVWLGTLGWALWEAGLDGWALLPRLGLLTGMGIVLAL-IRWRPGARTARIAATATAA 128

Query: 127 ALLISGGILTWAGFNDPQEINGTLSADATPAEAISPVADQDWPAYGRNQEGQRFSPLKQI 186
           A L++   L   G +     N +L   A+ A     VAD +W   GR     RFSPL QI
Sbjct: 129 AALLASISLVLTGSHG----NASLPLAASTAAG---VADGEWHHIGRTVGADRFSPLDQI 181

Query: 187 NADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGKE 246
              N+  L+ AW    G    P      T E TP+ VGDTLY C     + A+D  SGK 
Sbjct: 182 TPANIGKLQVAWTAHLG---MPPKGLAGTIEATPLMVGDTLYTCNMDNAVIAIDPDSGKT 238

Query: 247 KWHYDPELKTNESFQHVTCRGVSYHEAKAETASPEVMADCPRRIILPVNDGRLIAINAEN 306
           +W +DP+L   +  +   CRGV+YH        P +   C  RIIL   D RL A++A  
Sbjct: 239 RWAFDPKLNV-DGLKMTQCRGVTYHR------QPGISGPCAERIILTTYDNRLFALDAHG 291

Query: 307 GKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGSVTDNFSTRETSGVIR 366
           G+ C  F N G ++L   M     G Y  TSP  +    +++ G V D  +  E SGVIR
Sbjct: 292 GQRCRDFGNNGEVSLLDGMGGVPKGYYYQTSPAALVRDKLIVGGCVLDGQAVNEPSGVIR 351

Query: 367 GFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAKLDLVYLPMGVTTPD 426
            FD  TG L WA+D G  D   +P    T+T  +PN+W P + D +L L ++P+G  TPD
Sbjct: 352 AFDAVTGRLAWAWDMGRPDRQGLPPAGETYTRGTPNAWPPISGDDRLGLAFVPLGNPTPD 411

Query: 427 IWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPAQPTLADITVNGQKVP 486
               +RTPE  RY SS++AL+  TGK  W YQT H D+WD DLPA  +L D        P
Sbjct: 412 YVMSHRTPEMRRYGSSVVALDVETGKERWHYQTTHLDVWDYDLPAPASLVDFPTARGLRP 471

Query: 487 VIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPTQPFS-ELSFRPTKDLSG 545
            +  P K G  FVLDR  G+ +V   E+ VPQGAA G+ ++PTQP+   +       LS 
Sbjct: 472 ALIQPTKRGQFFVLDRETGKPLVETVERAVPQGAAPGESLSPTQPYPVGMPSLAGPRLSE 531

Query: 546 ADMWGATMFDQLVCRVMFHQMRYEGIFTP-PSEQGTLVFPGNLGMFEWGGISVDPNREVA 604
           A MWG T FDQ+ CR+ F Q RY+G FTP  +++ +++FPG  G   W GIS+DP R + 
Sbjct: 532 ARMWGITPFDQIWCRIRFRQARYDGDFTPVGTDKPSIIFPGMWGGSTWSGISIDPERRIM 591

Query: 605 IANPMALPFVSKLIPRGPGNPMEQPKDAKG-TGTESGIQPQYGVPYGVTLNPFLSPFGLP 663
           +AN    P  ++L+ R   +P E  +   G     S    Q G PY   + PF+SP  +P
Sbjct: 592 VANVNHFPMYNRLVRRADADPKEYQQFVAGRVAINSSRWSQTGTPYAAKVEPFMSPLKIP 651

Query: 664 CKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMPMLGGPISTAGNVL 723
           C QP +  I+A+DL    ++W+  +G  +++ PF +   VPF +G P LGG + T   ++
Sbjct: 652 CSQPPYSEIAAIDLGKRAMMWRHPVGRARNTGPFNIATGVPFVVGTPTLGGSMVTRSGLV 711

Query: 724 FIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYEV--NGKQYVVISAGGHGSFGTK 781
           FIAAT +   RAY++  G+ +W+ RLP  G   PMTY    +G+Q+V+I A GH  F   
Sbjct: 712 FIAATQEPAFRAYDLRTGKLVWETRLPTTGHGNPMTYRSPRSGRQFVLIPASGHPRFLNT 771

Query: 782 MGDYIVAYALPD 793
             D ++AYALP+
Sbjct: 772 ASDQLIAYALPE 783


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: 2063
Number of extensions: 126
Number of successful extensions: 14
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: 783
Length adjustment: 41
Effective length of query: 755
Effective length of database: 742
Effective search space:   560210
Effective search space used:   560210
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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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 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