Alignments for a candidate for gdh in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Stenotrophomonas chelatiphaga DSM 21508

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_057507612.1 ABB28_RS05160 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= BRENDA::D4P700
         (796 letters)



>NCBI__GCF_001431535.1:WP_057507612.1
          Length = 814

 Score =  561 bits (1447), Expect = e-164
 Identities = 329/818 (40%), Positives = 453/818 (55%), Gaps = 61/818 (7%)

Query: 16  VLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYALLLLATL 75
           +LFA+L G  +  GG+WL T+GGSW+Y++ GA +  T   L R  ++AL +   LLL   
Sbjct: 14  ILFALL-GVLLAAGGVWLITLGGSWFYLLAGAVLAATGVALVRLRASALWMALGLLLFAA 72

Query: 76  AWGVWEVGTDFWALAPRTDVLVIFGVWLVL--PFVYRGLYQPG-----KGAL-GAMGVAL 127
            W +WEVG DFW L PR    ++  +      P ++R    P       GAL G + + L
Sbjct: 73  VWALWEVGLDFWQLVPRLIAFLVVAMVTAAFAPRLHRRDLAPALRCRPAGALAGVLALGL 132

Query: 128 VASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTRFSPLKQ 187
           V   A +       P V      A   NA   Q   N    DWPAY R   G R++   Q
Sbjct: 133 VGFFAGMFVP---HPTVEADGSRAKVTNAAAGQAAGN----DWPAYGRTSSGDRYAQFDQ 185

Query: 188 INHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAATGK 247
           IN  NVK+LQVAW ++TGD+    D  E   +VTP+KI DT+YLCTP   + A+DA TGK
Sbjct: 186 INTTNVKDLQVAWTYRTGDLA--IDGAEY--QVTPLKIDDTVYLCTPLSKVVAVDATTGK 241

Query: 248 QKWKFDPGLKTNPTFQH-VTCRGVSYHEF--------------PAAKDASNTQ--PALCS 290
           +KW+FDP    + + Q    CRGV Y +               PA   A+NT   PA+C 
Sbjct: 242 EKWRFDPKAVVSESTQGWKRCRGVGYADLDALDTATAASTATAPAQAVAANTPAAPAICR 301

Query: 291 RRIYLPVNDGRLFALDAETGERCPAFGNNGELDL----QHKQPVTTPGMYEPTSPPVITD 346
           +RI     D RL ALDAETG+ C  FG+ G +DL          +  G Y  TS P++ D
Sbjct: 302 KRIIETTIDARLLALDAETGKLCEDFGDKGYVDLGIGIAPAPKDSDAGTYNVTSAPLVAD 361

Query: 347 TTIVMAGAVTDNFSTREPSGAIRGFDVNTGKLLWVFDP--GAKDPNAIPADEHTFTMNSP 404
             +++ G + DN +  EP G +RG+DV TGK+LW +D   GA D   +P  +  + + +P
Sbjct: 362 GVVMVGGRLNDNLTVGEPGGVVRGYDVVTGKILWAWDAKRGATDSTPLPEGQ-LYPLETP 420

Query: 405 NSWAPAVYDPKLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVH 464
           N W  A YDPKL + Y P+G  TPD W GNR    + Y  +V+A+   TGK  W ++T +
Sbjct: 421 NFWGTAAYDPKLGLAYFPLGNQTPDFWTGNRHDYSDEYTDAVVAVELKTGKERWHFRTAN 480

Query: 465 HDLWDMDLPSQPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGA 524
            D +D D+ SQP L D+  K+G T PV+    K G +FVLDRRTG+ VVP     V   A
Sbjct: 481 IDQFDYDVSSQPILYDMPGKNGETTPVLVQLTKRGQVFVLDRRTGQPVVPVEYRKVSTDA 540

Query: 525 AKGDHVSATQPYSELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSE-QG 583
             G  V+ TQP+S +     +   + DMWGA+++DQL CR+ FK++R+EG FTP S+ Q 
Sbjct: 541 MPGMKVAPTQPHSAIAV-GVEPFKESDMWGASIFDQLYCRIQFKQMRWEGEFTPLSDKQR 599

Query: 584 TLVFPGNLGMFEWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTE 643
           TL++PG  G F WGG +VD      I N + +    + I       +E  K       TE
Sbjct: 600 TLIYPGYYGGFNWGGGAVDASTGTLIVNDIRMAQWGRFI------KQEEAKRIGYKPSTE 653

Query: 644 TGIQPQYGVPYGVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPV- 702
                Q G P+GVE + F+SP G+PC +P +G ++A+DL T +  W+  +GT++D +PV 
Sbjct: 654 GEYSTQTGTPWGVERSMFVSPLGVPCFKPPFGTMTAIDLSTGKTRWQVPMGTIKD-APVH 712

Query: 703 ----PLPFKMGMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATP 758
                +   +GMP +GGP+ T G + F   + D Y+RA   DTG++LWQ RLP GGQ  P
Sbjct: 713 GIAPGVDIPLGMPTMGGPLVTKGGLTFFHGSLDYYVRALDNDTGKVLWQGRLPVGGQGAP 772

Query: 759 MTY-EVNGKQYVVIAAGGHGSFGT--KLGDYVIAYALP 793
           M+Y   +G+QYVV+ AGG    GT    GDYVIAYALP
Sbjct: 773 MSYVGKDGRQYVVVVAGGATRTGTNDNRGDYVIAYALP 810


Lambda     K      H
   0.319    0.137    0.433 

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: 2217
Number of extensions: 145
Number of successful extensions: 22
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 796
Length of database: 814
Length adjustment: 41
Effective length of query: 755
Effective length of database: 773
Effective search space:   583615
Effective search space used:   583615
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: 56 (26.2 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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