Alignments for a candidate for sdh in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Dyella japonica UNC79MFTsu3.2

Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate N515DRAFT_0461 N515DRAFT_0461 quinoprotein glucose dehydrogenase

Query= BRENDA::Q70JN9
         (743 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0461
          Length = 816

 Score =  503 bits (1294), Expect = e-146
 Identities = 280/680 (41%), Positives = 377/680 (55%), Gaps = 55/680 (8%)

Query: 96  APQQSASPASG------DWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPRPG 149
           AP+  A PA        DW AYG      R++P ++ITP N  +L+VA+ +HTG +  PG
Sbjct: 154 APEAGAPPADATGTPPNDWIAYGRSGHGDRHAPAAQITPANVAKLQVAWTFHTGDFKGPG 213

Query: 150 QTNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYT-AACKGV 208
              + A E TP+K    LY+C+  + ++ +DP TGKE WR++     +A  Y    C+GV
Sbjct: 214 DPTEIANEVTPLKANGMLYLCTPHDIVIALDPDTGKERWRYDPKINRDAKGYQHMICRGV 273

Query: 209 TYF----------TSSQVPEGQP----------------CHNRILEGTLDMRLIAVDAAT 242
            Y           T+   P   P                C  RI   T D  ++A++A  
Sbjct: 274 AYHDSGAYAAQAATAGVAPAAPPPTPKGAVAAEAIHFDSCPRRIFAPTADATVVALNADN 333

Query: 243 GNLCEGFGNGGQVNLMQGLGESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIR 302
           G  C  FG+ G + L QG+     GF++ T+PP V   V++V+  V D +    PSGVIR
Sbjct: 334 GQPCTDFGDHGVIGLYQGMAMKRRGFLNPTSPPTVTRNVLIVSASVTDNESTDEPSGVIR 393

Query: 303 GYDAESGKFLWAWDVNRPNDHSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASD 362
           GYD  +G+ LW WD   P+  +      HY R +PNSW+  + D  LGLVY+P GN   D
Sbjct: 394 GYDVTTGQLLWNWDAAAPDSTAPLPAGQHYKRNSPNSWSVSSVDEKLGLVYIPMGNQTPD 453

Query: 363 YYSALRSPEENKVSSAVVALDVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPV 422
            +   R PE  + +SA+VALD+ TG  RWV+QTVH D+WD DIG Q +L+D+    G+ V
Sbjct: 454 MWGGERYPEGERFNSAIVALDIATGKLRWVYQTVHHDLWDMDIGGQPSLVDLDTPQGK-V 512

Query: 423 PALIMPTKRGQTFVLDRRDGKPILPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDL 482
           PAL+  TKRG  +VLDRRDGKP++P  ERP P  G   GD  SPTQP+S    A   P L
Sbjct: 513 PALVASTKRGDIYVLDRRDGKPVVPAPERPVPQ-GAATGDRTSPTQPFSALSFAPEHP-L 570

Query: 483 KETDMWGMSPIDQLFCRIKFRRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSG 542
           +E DMWG +P DQL CRIKFRR  Y G FTPPS ++  + YPG  G  DWG V+ DPQ  
Sbjct: 571 READMWGTNPYDQLVCRIKFRRLRYDGIFTPPS-EQGSLVYPGNYGVFDWGGVTVDPQRQ 629

Query: 543 ILIANWNITPMYDQLVTRKKADELGLMPIDDPNYKPGGGGAE-GNGAMDGTPYGIVVTPF 601
           +LI N N      +L+TR+          ++     G  G E G   M GTP+ + + P 
Sbjct: 630 LLIGNPNYMAFMSRLITRE---------TEEARSAKGSTGIEHGLQPMQGTPFAVDLRPL 680

Query: 602 WDQYTGMMCNRPPYGMITAIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGG 661
                G+ C  PP+G + A+D++  +K LW H  GT   + P  LP  LP  +G P+ GG
Sbjct: 681 LSP-LGIPCQAPPWGYVAAVDLRTMRK-LWMHRNGTVVDSAP--LPIPLP--LGVPSLGG 734

Query: 662 SVVTAGGVVFIAAATDNQIRAIDEHTGKVVWSAVLPGGGQANPMTY--EANGHQYVAIMA 719
            + T GGV F++A+ D  +RA D   GK +W A LP GGQA PM+Y  +  G QYV IMA
Sbjct: 735 MITTGGGVAFMSASLDYYLRAYDVRNGKQLWEARLPAGGQATPMSYVSDQTGRQYVVIMA 794

Query: 720 GGHHFMMTPVSDQLVVYALP 739
           GGH  + T + D L+ YALP
Sbjct: 795 GGHGSLGTKMGDALIAYALP 814


Lambda     K      H
   0.315    0.134    0.428 

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: 2297
Number of extensions: 159
Number of successful extensions: 12
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: 743
Length of database: 816
Length adjustment: 41
Effective length of query: 702
Effective length of database: 775
Effective search space:   544050
Effective search space used:   544050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)

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

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Steps (tab-delimited)
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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 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