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_057687398.1 ABB28_RS16160 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= BRENDA::D4P700
         (796 letters)



>NCBI__GCF_001431535.1:WP_057687398.1
          Length = 797

 Score =  607 bits (1566), Expect = e-178
 Identities = 340/809 (42%), Positives = 463/809 (57%), Gaps = 42/809 (5%)

Query: 9   SVVRFLTVLFAVLTGAF---MLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALV 65
           +V R L +L  +L   F   +L+GG+ L T+GGS Y+ + GA  LL   LL  R     +
Sbjct: 9   AVCRVLVILLGILVSLFGLTLLVGGVRLLTLGGSAYFALMGAITLLAGVLLVLRRPLGAL 68

Query: 66  VYALLLLATLAWGVWEVGTDFWALAPRTDVLVIFGVWLVL--PFVYRGLYQP-GKGALGA 122
           ++    +ATL W V + G +FW L  R  +  +  + + L  P + R    P G+G    
Sbjct: 69  LFGGAFVATLVWSVVDAGLEFWPLVSRLVMPAVLAMLVALSWPVLRRSRGLPAGRGGYAV 128

Query: 123 MGVALVASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADG-DWPAYARDQQGTR 181
             + LV        +    P V      A A   P   P++  ++  DW  +     GTR
Sbjct: 129 AALLLVGLLGTGAAAFQPRPVV------AAAGTRPAVTPVAAGSEQRDWAHWGNTTAGTR 182

Query: 182 FSPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFAL 241
           F+ L QI  DNV +LQVAW  +TGD+   +  G   D+ TP++I DTL+LCTPH  + A+
Sbjct: 183 FAALDQITLDNVDQLQVAWTARTGDVPESNGFGA-EDQNTPLQIGDTLFLCTPHNRVIAV 241

Query: 242 DAATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEF-------PAAKDASNTQPALCSRRIY 294
           DA TGKQ+W FDP   T P +Q   CRG+ Y +        P A  AS T PALC +RI 
Sbjct: 242 DADTGKQRWAFDPKA-TAPNWQR--CRGLGYFDADLAPAPAPVAGVASPTAPALCRKRIL 298

Query: 295 LPVNDGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGA 354
           +   D RLFALDA TG  CP FG+NG +DL+       PG +  T+ P++    IV+ G 
Sbjct: 299 MTSIDARLFALDAATGAPCPDFGSNGVVDLKQGMGEIKPGFFTITAAPLVAGELIVVGGR 358

Query: 355 VTDNFSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHT-FTMNSPNSWAPAVYD 413
           V DN    EPSG +R F+V TG L WV+D   + P+ +P D    +T  +PN W    YD
Sbjct: 359 VADNIEVNEPSGVVRAFNVRTGALAWVWDLSRETPD-VPLDPSVEYTRATPNVWTSMAYD 417

Query: 414 PKLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLP 473
            +L +VYLP G TTPD W G RTP+ ++Y+S+V+AL+  TGK  W YQTVHHDLWD DLP
Sbjct: 418 AQLGLVYLPTGNTTPDQWAGQRTPQDDKYSSAVVALDVATGKERWVYQTVHHDLWDYDLP 477

Query: 474 SQPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSAT 533
           +QPTL D+ D  G T+P +    K G +F+L+R+TG+ +    + P PQG A+G+  S T
Sbjct: 478 AQPTLTDVPDGKGGTLPALLQVTKAGQVFMLNRQTGQPIAAVQDIPAPQGKAQGERYSPT 537

Query: 534 QPYS-ELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLG 592
           Q  S  L     Q LT+ DMWGAT  DQ++CR+ FK+ RY+G FTPP E   L +PG+LG
Sbjct: 538 QRLSVGLPQIGAQTLTESDMWGATPIDQMLCRIQFKQFRYDGMFTPPGEDLALQWPGSLG 597

Query: 593 MFEWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGV 652
              WG  SVDP       N M L   +KLIPR         +  +G  G E G   Q G 
Sbjct: 598 GMNWGSASVDPTTGYLFVNDMRLGLWTKLIPRA--------QMTSGDGGVEMGAASQTGT 649

Query: 653 PYGVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSP----VPLPFKM 708
           PYG   + FLS  G+PC++P +G +SA++L T ++VW+  +GTV+D+ P    + LP  +
Sbjct: 650 PYGSLRDRFLSKLGIPCQKPPFGTMSAINLATRQLVWQVPVGTVQDTGPLGIRMHLPIPV 709

Query: 709 GMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTY--EVNGK 766
           GMP LGG +AT   + F   T D YLRA+ + +G+ +W+ARLP G Q TP+TY     G+
Sbjct: 710 GMPTLGGSLATQSGLLFFAGTQDFYLRAYDSRSGKEVWKARLPVGSQGTPITYVSPTTGR 769

Query: 767 QYVVIAAGGHGSFGTKLGDYVIAYALPDQ 795
           QYVVI+AGG      + GDYVIAYALP +
Sbjct: 770 QYVVISAGGARQSPDR-GDYVIAYALPSK 797


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: 2231
Number of extensions: 162
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: 797
Length adjustment: 41
Effective length of query: 755
Effective length of database: 756
Effective search space:   570780
Effective search space used:   570780
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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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