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_038216754.1 Q392_RS28530 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= BRENDA::Q70JN9
         (743 letters)



>NCBI__GCF_000745855.1:WP_038216754.1
          Length = 821

 Score =  476 bits (1224), Expect = e-138
 Identities = 270/690 (39%), Positives = 377/690 (54%), Gaps = 53/690 (7%)

Query: 85  GSMDPNDVPQMAPQQSASPASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGS 144
           G ++        P+ +A    G+W AYG      R+SPL++ITP NA+QL++A+ + TG 
Sbjct: 147 GRLESRPAADAVPETAAPVPPGEWHAYGRTGEGQRHSPLAQITPANANQLRLAWEFRTGD 206

Query: 145 YP-RPGQTNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTA 203
              RPG   +   E TP+K+G+ L++C+    ++ +D  TG+++WR +     +      
Sbjct: 207 RRGRPGDPEETTYEVTPLKIGNRLFLCTPHQSVIALDATTGRQLWRFDPQIAGDLALQHL 266

Query: 204 ACKGVTYFTSSQVPEGQP------------------------------CHNRILEGTLDM 233
            C+G++Y     VP   P                              C +R+   T D 
Sbjct: 267 TCRGLSYQPPRAVPAPSPAPTAGEGRAEPATERPPLPVAASQGATDPACRSRLFMPTADG 326

Query: 234 RLIAVDAATGNLCEGFGNG-GQVNLMQGLGESVPGFVSMTTPPPVVNGVVVVNHEVLDGQ 292
           RLIA++  +G +C  FGNG GQ++L Q +    PG    T+PP V   +++V   VLD  
Sbjct: 327 RLIALNPDSGAVCTDFGNGTGQIDLWQHMPNVRPGAYYSTSPPVVTERLLIVGGTVLDNA 386

Query: 293 RRWAPSGVIRGYDAESGKFLWAWDVNRPNDHSQPTGNNHYSRGTPNSWAAMTGDNALGLV 352
                SGVIR +D +SG  +W WD   P+D +       Y+  +PNSW+  + D ALG+V
Sbjct: 387 SVKEQSGVIRAFDIDSGALVWNWDSGNPDDTAPLPPGRTYTANSPNSWSVSSVDEALGMV 446

Query: 353 YVPTGNSASDYYSALRSPEENKVSSAVVALDVKTGSPRWVFQTVHKDVWDYDIGSQATLM 412
           YVP GN   D +   RSP   + +S+VVALD+ +G  RW FQTVH D+WDYD+ +Q TL+
Sbjct: 447 YVPMGNQPPDQWGGHRSPAVERYASSVVALDLASGRVRWHFQTVHHDLWDYDVPAQPTLL 506

Query: 413 DMPGQDGQPVPALIMPTKRGQTFVLDRRDGKPILPVEERPAPSPGVIPGDPRSPTQPWST 472
           DM    G+ VPAL+ PTK+G+ FVLDRRDG P+LPV E+PAP  G   GD  +PTQP S 
Sbjct: 507 DME-VGGRRVPALVQPTKQGELFVLDRRDGTPLLPVSEQPAPQ-GAAAGDHTAPTQPASA 564

Query: 473 GMPALRVPDLKETDMWGMSPIDQLFCRIKFRRANYTGEFTPPSVDKPWIEYPGYNGGSDW 532
              +   P L+E DMWG + +DQL CRI FR+  Y G FTPPS ++  I YPG  G  +W
Sbjct: 565 --LSFAPPPLRERDMWGATLLDQLACRIAFRQLRYEGRFTPPS-ERGSIVYPGNFGVFNW 621

Query: 533 GSVSYDPQSGILIANWNITPMYDQLVTR--KKADELGLMPIDDPNYKPGGGGAEGNGAMD 590
           G ++ DP  G        TP Y   V+R   + D++ L+  +     P  G         
Sbjct: 622 GGIAVDPARGWAFT----TPTYLAFVSRLVARRDDISLLVQEG---GPPKGSLPALNENF 674

Query: 591 GTPYGIVVTPFWDQYTGMMCNRPPYGMITAIDMKHGQKVLWQHPLGTARANGPWGLPTGL 650
           G PY   + PF     G+ C  PP+G +  +D++ GQ V W+H  GT R   P  LP  L
Sbjct: 675 GAPYAASMKPFMSP-VGLPCQAPPWGYVAGVDLRTGQ-VAWKHRNGTVRDLSP--LP--L 728

Query: 651 PWEIGTPNNGGSVVTAGGVVFIAAATDNQIRAIDEHTGKVVWSAVLPGGGQANPMTYEA- 709
           P+ +G P  GG +VTAGGV F + A DN +RA D  +G+V+WS  LP GGQA PMTY   
Sbjct: 729 PFRMGVPGIGGPMVTAGGVAFYSGALDNYVRAYDMASGRVLWSDRLPAGGQATPMTYSGE 788

Query: 710 NGHQYVAIMAGGHHFMMTPVSDQLVVYALP 739
           +G QYV ++AGGH    T   D +  YALP
Sbjct: 789 DGRQYVLVVAGGHGSTGTKPGDAIRAYALP 818


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: 2283
Number of extensions: 155
Number of successful extensions: 14
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 2
Length of query: 743
Length of database: 821
Length adjustment: 41
Effective length of query: 702
Effective length of database: 780
Effective search space:   547560
Effective search space used:   547560
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