Alignments for a candidate for gdh in Xenophilus azovorans DSM 13620

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Xenophilus azovorans DSM 13620

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate WP_038210510.1 Q392_RS17500 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= CharProtDB::CH_002195
         (796 letters)



>NCBI__GCF_000745855.1:WP_038210510.1
          Length = 773

 Score =  569 bits (1467), Expect = e-166
 Identities = 330/797 (41%), Positives = 453/797 (56%), Gaps = 53/797 (6%)

Query: 17  ALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRA-ALWLYAALLLGT 75
           AL  AL GL L +GG  L+ +GGS YY  AGLV+L  A  +WR +R+ ALW+ AAL + T
Sbjct: 9   ALLVALMGLGLALGGARLLLLGGSPYYVAAGLVLLWAALQMWRRRRSSALWV-AALAVLT 67

Query: 76  MIWGVWEVGFDFWALTPRSDI-LVFFGIWLILP---------FVWRRLVIPASGAVAALV 125
           + W +WE G DFWAL PR    L    + L+L            WR      +GAV AL+
Sbjct: 68  LPWALWESGLDFWALFPRLMAPLALAAVSLLLAPRAPEGGSAAPWR-----LAGAVFALL 122

Query: 126 VALLISGGILTWAGFNDPQEINGTLSADATPAEAISPVADQ---DWPAYGRNQEGQRFSP 182
             L          GF      +G +  DA+ A    P  D    DW AYGR  EG+R +P
Sbjct: 123 FVL----------GFGLAFMPHGVVRPDASMAYT-PPGGDNRPVDWSAYGRTTEGRRDAP 171

Query: 183 LKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAA 242
             QIN + V  LK AW +RTGD +    PG   N  TP+++GD +Y CT + +L ALDA 
Sbjct: 172 FDQINRETVSQLKLAWSYRTGDTQ----PGVDQN--TPLQIGDLVYSCTRNDKLIALDAD 225

Query: 243 SGKEKWHYDPELKTNESFQHVTCRGVSYHEAKAETASPEVMADCPRRIILPVNDGRLIAI 302
           SG+E+W +DP+ K+   +Q   CRG+ Y +A  E A+    A C  RI+    D RLI +
Sbjct: 226 SGQERWVFDPQAKS-PFWQR--CRGLGYWKAPQEAAAAPEGA-CRERIVQTTIDARLIEL 281

Query: 303 NAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGSVTDNFSTRETS 362
           +A  GK CE F +KG ++L   M   +PG Y  TS P++    IV+ G V DN    E S
Sbjct: 282 DARTGKPCEEFGDKGTVSLAHGMGTVRPGFYFQTSAPLVARDLIVVGGWVVDNQMRGEPS 341

Query: 363 GVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAKLDLVYLPMGV 422
           GVIR F   TGEL+WA+D G  D   +P +  T+T  +PN W  AAYD KL L+Y P+G 
Sbjct: 342 GVIRAFSARTGELVWAWDLGNPDITKLPPEGQTYTPGTPNMWTTAAYDDKLGLIYAPLGN 401

Query: 423 TTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPAQPTLADI-TVN 481
            TPD +G  R    + Y ++++AL+  TG+  W +QTVHHD+WD DLP+QP L D+    
Sbjct: 402 ATPDYFGQGRPAHSDEYNATLVALDVATGRPRWKFQTVHHDIWDYDLPSQPALIDLPDGK 461

Query: 482 GQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQ-GAAKGDYVTPTQPFS-ELSFRP 539
           G  VP +    K G +F+LDR  G+ +    EKPV Q GA   + ++PTQP+S  +    
Sbjct: 462 GGTVPAVLQTTKRGQLFLLDRATGQPLAEVAEKPVTQEGAVPEETLSPTQPYSVGMPTVG 521

Query: 540 TKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGMFEWGGISVDP 599
            + L    MWG TMFDQL+CR+ F  +RY+G FTPP  Q  +  PGN+G   WG +SVD 
Sbjct: 522 AERLDERRMWGMTMFDQLLCRIEFRTLRYDGDFTPPGLQRAIEHPGNVGGLNWGSVSVDT 581

Query: 600 NREVAIANPMALPFVSKLIPRG--PGNPMEQPKDAKGTGTESGIQPQYGVPYGVTLNPFL 657
             +    N + +P V +L+PR   P    + P  + G G  +    Q G PYG+    + 
Sbjct: 582 ANQRVFLNDIRVPSVFQLVPRDDYPAFAKKYPPVSDGHGPST----QAGTPYGIYTTIWF 637

Query: 658 SPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMPMLGGPIS 717
           S  G+PC QP +G ++A+DLKT +V W+   GT +   P  + + +P  +GMP   G ++
Sbjct: 638 SRLGVPCVQPPFGTLTAIDLKTRKVAWQVPAGTAEQLGPLGVRLGLPMPIGMPTYAGTLA 697

Query: 718 TAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTY--EVNGKQYVVISAGGH 775
           TAG ++F A T D YLRAY+   G ++W+  +P G  ATPMTY     GKQYVVISAGG 
Sbjct: 698 TAGGLVFFAGTQDFYLRAYDAQTGAEVWKHAMPVGSSATPMTYVSPRTGKQYVVISAGG- 756

Query: 776 GSFGTKMGDYIVAYALP 792
            ++  + GDY++A+ALP
Sbjct: 757 AAYSKERGDYVMAFALP 773


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: 2198
Number of extensions: 133
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: 773
Length adjustment: 41
Effective length of query: 755
Effective length of database: 732
Effective search space:   552660
Effective search space used:   552660
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