Alignments for a candidate for gdh in Snodgrassella alvi wkB2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Snodgrassella alvi wkB2

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_025329982.1 SALWKB2_RS01815 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= BRENDA::D4P700
         (796 letters)



>NCBI__GCF_000600005.1:WP_025329982.1
          Length = 802

 Score =  576 bits (1485), Expect = e-168
 Identities = 338/811 (41%), Positives = 471/811 (58%), Gaps = 48/811 (5%)

Query: 12  RFLTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYALLL 71
           R+L VL  +  G  +  GGI L  +GGS YY++ G A L+ + ++  R S   +    + 
Sbjct: 14  RWLLVLILLAGGLALGYGGIKLLILGGSGYYLLAGIAYLVLSIMVGLRKSYTALFSLAVF 73

Query: 72  LATLAWGVWEVGT-DFWALAPRTDVLVIFGVWLVLPFV----YRGLYQPGKGALGAMGVA 126
           +ATL W + +     +WAL PR   LVI  ++L++       Y+G+   G+      GV 
Sbjct: 74  VATLIWALTDATELTYWALMPR---LVIPALFLMMTLWSGSGYQGVSASGRRFYNFSGVV 130

Query: 127 L-VASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTRFSPL 185
           + +A  A L  S +   Q+ N      ++NA  A   +     DW  + R+Q+GTRF+P 
Sbjct: 131 IFLALLATLIASFYPHGQIRNQV--NISENADAAHENAQ-NPSDWAFFGRNQRGTRFAPY 187

Query: 186 KQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAAT 245
            QIN DNV+ LQVAW F TG  +R S      DE TP++I D LY CTP  ++ A+DA T
Sbjct: 188 SQINPDNVRNLQVAWTFHTG--RRTSGKAIGVDENTPLQIGDKLYSCTPENLVSAIDADT 245

Query: 246 GKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPA-----LCSRRIYLPVNDG 300
           GK  W+FDP  +T    +HVTCRGV Y++       +N + A     +C RRI +   D 
Sbjct: 246 GKLIWRFDPKARTA---EHVTCRGVGYYDMDKDDSLTNAEKAAYTQSVCRRRIVVSTVDA 302

Query: 301 RLFALDAETGERCPAFGNNGELDLQ-HKQPVTTPGMYEPTSPPVITDTTIVMAGAVTDNF 359
           RLF LDA+ G  CP FG+NG ++L+ +  P      Y PTS PV+     V+ G V D  
Sbjct: 303 RLFTLDADKGTLCPGFGDNGYVNLKAYMGPTENSKRYHPTSLPVMMGHLTVVGGWVRD-I 361

Query: 360 STREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDIV 419
              EPSGA+R FDV  GKL+W +D G  +  A P     +T+ +PN W    YD +L++V
Sbjct: 362 VHGEPSGAVRAFDVRDGKLVWTWDIGKPEGLAKPGQN--YTLETPNVWTIPTYDKELNLV 419

Query: 420 YLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTLA 479
           YLP G   PD WGG+R   +E++ ++V+AL+A+TGKL W  Q VHHD+WD DLPSQP L 
Sbjct: 420 YLPTGNGPPDYWGGDRNHIKEKFGAAVVALDASTGKLRWVRQLVHHDVWDYDLPSQPVLY 479

Query: 480 DITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQG-AAKGDHVSATQPYS- 537
           D+T+  G  +P +    KTG IFV+DRR G+ V    E+PVP   AA+G+H+SATQP S 
Sbjct: 480 DVTNDKGQKIPALIQTTKTGQIFVIDRRNGEFVTKVVESPVPTAPAAEGEHLSATQPDSV 539

Query: 538 ELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFEWG 597
            +     + LT++ MWG T +DQL CR++FK   Y+G FTPPS Q  + +P  LG   WG
Sbjct: 540 GMPNIGNEPLTERSMWGITPFDQLYCRILFKNSVYKGRFTPPSAQPYIEWPSLLGGMNWG 599

Query: 598 GISVDPHRQIAIANPMALPFVSKLIPRGPG-----NPEEPPKGATGGSGTETGIQPQY-G 651
           GIS+D  R +   N M +    +L+ R        + +E P    G  GT   I+PQ  G
Sbjct: 600 GISIDESRNLMFVNDMRMALRMQLVTREEAKQFKVSTDEVP----GFMGT---IRPQVAG 652

Query: 652 VPYGVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPL----PFK 707
           +  GV+++   SP G+PC+QP +G +SA+DL T ++VW+  +GTV+D+ P+ +    P  
Sbjct: 653 IYGGVKIDILQSPLGVPCQQPPFGTLSAIDLNTKQLVWQVPMGTVQDTGPLNIKTKQPMP 712

Query: 708 MGMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTY--EVNG 765
           +GMP LGGP ATA  + F   T D YLRA    TG+ +W+ARLP G  A P+ Y     G
Sbjct: 713 IGMPTLGGPTATASGLVFFAGTQDYYLRAIDAKTGKEVWKARLPVGSVAAPLIYVSPKTG 772

Query: 766 KQYVVIAAGGHGSFGTKLGDYVIAYALPDQK 796
           K+YVVI+AGG  S    +GDYVIAYALPD+K
Sbjct: 773 KEYVVISAGG-TSHSNDVGDYVIAYALPDKK 802


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: 2121
Number of extensions: 137
Number of successful extensions: 23
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: 802
Length adjustment: 41
Effective length of query: 755
Effective length of database: 761
Effective search space:   574555
Effective search space used:   574555
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.

Downloads

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

Related tools

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