Alignments for a candidate for sdh in Xenophilus azovorans DSM 13620

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Xenophilus azovorans DSM 13620

Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate WP_038210510.1 Q392_RS17500 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= BRENDA::Q70JN9
         (743 letters)



>NCBI__GCF_000745855.1:WP_038210510.1
          Length = 773

 Score =  489 bits (1260), Expect = e-142
 Identities = 270/662 (40%), Positives = 365/662 (55%), Gaps = 32/662 (4%)

Query: 89  PNDVPQMAPQQSASPASGD-----WAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTG 143
           P+ V +     + +P  GD     W+AYG      R +P  +I  +   QLK+A+ Y TG
Sbjct: 133 PHGVVRPDASMAYTPPGGDNRPVDWSAYGRTTEGRRDAPFDQINRETVSQLKLAWSYRTG 192

Query: 144 SYPRPGQTNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTA 203
                  T     + TP+++GD +Y C+  + ++ +D  +G+E W  +   K    P+  
Sbjct: 193 D------TQPGVDQNTPLQIGDLVYSCTRNDKLIALDADSGQERWVFDPQAKS---PFWQ 243

Query: 204 ACKGVTYFTSSQ----VPEGQPCHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLMQ 259
            C+G+ Y+ + Q     PEG  C  RI++ T+D RLI +DA TG  CE FG+ G V+L  
Sbjct: 244 RCRGLGYWKAPQEAAAAPEGA-CRERIVQTTIDARLIELDARTGKPCEEFGDKGTVSLAH 302

Query: 260 GLGESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVNR 319
           G+G   PGF   T+ P V   ++VV   V+D Q R  PSGVIR + A +G+ +WAWD+  
Sbjct: 303 GMGTVRPGFYFQTSAPLVARDLIVVGGWVVDNQMRGEPSGVIRAFSARTGELVWAWDLGN 362

Query: 320 PNDHSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSAV 379
           P+    P     Y+ GTPN W     D+ LGL+Y P GN+  DY+   R    ++ ++ +
Sbjct: 363 PDITKLPPEGQTYTPGTPNMWTTAAYDDKLGLIYAPLGNATPDYFGQGRPAHSDEYNATL 422

Query: 380 VALDVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTFVLDR 439
           VALDV TG PRW FQTVH D+WDYD+ SQ  L+D+P   G  VPA++  TKRGQ F+LDR
Sbjct: 423 VALDVATGRPRWKFQTVHHDIWDYDLPSQPALIDLPDGKGGTVPAVLQTTKRGQLFLLDR 482

Query: 440 RDGKPILPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDLKETDMWGMSPIDQLFCR 499
             G+P+  V E+P    G +P +  SPTQP+S GMP +    L E  MWGM+  DQL CR
Sbjct: 483 ATGQPLAEVAEKPVTQEGAVPEETLSPTQPYSVGMPTVGAERLDERRMWGMTMFDQLLCR 542

Query: 500 IKFRRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYDQLVT 559
           I+FR   Y G+FTPP + +  IE+PG  GG +WGSVS D  +  +  N    P   QLV 
Sbjct: 543 IEFRTLRYDGDFTPPGLQRA-IEHPGNVGGLNWGSVSVDTANQRVFLNDIRVPSVFQLVP 601

Query: 560 RKKADELGLMPIDDPNYKPGGGGAEGNGAMDGTPYGIVVTPFWDQYTGMMCNRPPYGMIT 619
           R         P     Y P   G  G     GTPYGI  T  W    G+ C +PP+G +T
Sbjct: 602 RDD------YPAFAKKYPPVSDG-HGPSTQAGTPYGIYTT-IWFSRLGVPCVQPPFGTLT 653

Query: 620 AIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAAATDNQ 679
           AID+K  +KV WQ P GTA   GP G+  GLP  IG P   G++ TAGG+VF A   D  
Sbjct: 654 AIDLK-TRKVAWQVPAGTAEQLGPLGVRLGLPMPIGMPTYAGTLATAGGLVFFAGTQDFY 712

Query: 680 IRAIDEHTGKVVWSAVLPGGGQANPMTYEA--NGHQYVAIMAGGHHFMMTPVSDQLVVYA 737
           +RA D  TG  VW   +P G  A PMTY +   G QYV I AGG  +      D ++ +A
Sbjct: 713 LRAYDAQTGAEVWKHAMPVGSSATPMTYVSPRTGKQYVVISAGGAAYSKER-GDYVMAFA 771

Query: 738 LP 739
           LP
Sbjct: 772 LP 773


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: 2108
Number of extensions: 160
Number of successful extensions: 8
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: 773
Length adjustment: 40
Effective length of query: 703
Effective length of database: 733
Effective search space:   515299
Effective search space used:   515299
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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 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