Alignments for a candidate for sdh in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Stenotrophomonas chelatiphaga DSM 21508

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

Query= BRENDA::Q70JN9
         (743 letters)



>NCBI__GCF_001431535.1:WP_057687398.1
          Length = 797

 Score =  477 bits (1228), Expect = e-139
 Identities = 262/657 (39%), Positives = 371/657 (56%), Gaps = 41/657 (6%)

Query: 100 SASPASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPRPGQTNKWAAE-- 157
           +A     DWA +G+  +  R++ L +IT  N DQL+VA+   TG  P   ++N + AE  
Sbjct: 163 AAGSEQRDWAHWGNTTAGTRFAALDQITLDNVDQLQVAWTARTGDVP---ESNGFGAEDQ 219

Query: 158 TTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTAACKGVTYFTSSQVP 217
            TP+++GD L++C+  N ++ +D  TGK+ W     +     P    C+G+ YF +   P
Sbjct: 220 NTPLQIGDTLFLCTPHNRVIAVDADTGKQRWAF---DPKATAPNWQRCRGLGYFDADLAP 276

Query: 218 EGQP------------CHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLMQGLGESV 265
              P            C  RIL  ++D RL A+DAATG  C  FG+ G V+L QG+GE  
Sbjct: 277 APAPVAGVASPTAPALCRKRILMTSIDARLFALDAATGAPCPDFGSNGVVDLKQGMGEIK 336

Query: 266 PGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVNRPNDHSQ 325
           PGF ++T  P V   ++VV   V D      PSGV+R ++  +G   W WD++R      
Sbjct: 337 PGFFTITAAPLVAGELIVVGGRVADNIEVNEPSGVVRAFNVRTGALAWVWDLSRETPDVP 396

Query: 326 PTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSAVVALDVK 385
              +  Y+R TPN W +M  D  LGLVY+PTGN+  D ++  R+P+++K SSAVVALDV 
Sbjct: 397 LDPSVEYTRATPNVWTSMAYDAQLGLVYLPTGNTTPDQWAGQRTPQDDKYSSAVVALDVA 456

Query: 386 TGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTFVLDRRDGKPI 445
           TG  RWV+QTVH D+WDYD+ +Q TL D+P   G  +PAL+  TK GQ F+L+R+ G+PI
Sbjct: 457 TGKERWVYQTVHHDLWDYDLPAQPTLTDVPDGKGGTLPALLQVTKAGQVFMLNRQTGQPI 516

Query: 446 LPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDLKETDMWGMSPIDQLFCRIKFRRA 505
             V++ PAP  G   G+  SPTQ  S G+P +    L E+DMWG +PIDQ+ CRI+F++ 
Sbjct: 517 AAVQDIPAPQ-GKAQGERYSPTQRLSVGLPQIGAQTLTESDMWGATPIDQMLCRIQFKQF 575

Query: 506 NYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYDQLVTRKKADE 565
            Y G FTPP  D   +++PG  GG +WGS S DP +G L  N     ++ +L+ R +   
Sbjct: 576 RYDGMFTPPGEDLA-LQWPGSLGGMNWGSASVDPTTGYLFVNDMRLGLWTKLIPRAQMTS 634

Query: 566 LGLMPIDDPNYKPGGGGAE-GNGAMDGTPYGIVVTPFWDQYTGMMCNRPPYGMITAIDMK 624
                        G GG E G  +  GTPYG +   F  +  G+ C +PP+G ++AI++ 
Sbjct: 635 -------------GDGGVEMGAASQTGTPYGSLRDRFLSK-LGIPCQKPPFGTMSAINLA 680

Query: 625 HGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAAATDNQIRAID 684
             Q ++WQ P+GT +  GP G+   LP  +G P  GGS+ T  G++F A   D  +RA D
Sbjct: 681 TRQ-LVWQVPVGTVQDTGPLGIRMHLPIPVGMPTLGGSLATQSGLLFFAGTQDFYLRAYD 739

Query: 685 EHTGKVVWSAVLPGGGQANPMTY--EANGHQYVAIMAGGHHFMMTPVSDQLVVYALP 739
             +GK VW A LP G Q  P+TY     G QYV I AGG         D ++ YALP
Sbjct: 740 SRSGKEVWKARLPVGSQGTPITYVSPTTGRQYVVISAGGAR-QSPDRGDYVIAYALP 795


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: 2006
Number of extensions: 132
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: 797
Length adjustment: 41
Effective length of query: 702
Effective length of database: 756
Effective search space:   530712
Effective search space used:   530712
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 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