Alignments for a candidate for gadh1 in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for gadh1 in Stenotrophomonas chelatiphaga DSM 21508

Align Gluconate 2-dehydrogenase flavoprotein; GA 2-DH dehydrogenase subunit; GADH dehydrogenase subunit; EC 1.1.99.3 (characterized)
to candidate WP_057507641.1 ABB28_RS05330 GMC family oxidoreductase

Query= SwissProt::O34214
         (615 letters)



>NCBI__GCF_001431535.1:WP_057507641.1
          Length = 591

 Score =  712 bits (1837), Expect = 0.0
 Identities = 339/588 (57%), Positives = 419/588 (71%), Gaps = 3/588 (0%)

Query: 28  KVDAVVVGFGWAGAIMAKELTEAGLNVVALERGPHRDTYPDGAYPQSIDELTYNIRKKLF 87
           KVD ++VG GW GAIMAKELT+AGL+VVALERG  RDT PD AYP  +DEL  ++ ++  
Sbjct: 7   KVDVLIVGMGWTGAIMAKELTDAGLHVVALERGGDRDTQPDFAYPNVVDELEGSVHRRYL 66

Query: 88  QDLSKSTVTIRHDASQTAVPYRQLAAFLPGTGTGGAGLHWSGVHFRVDPVELNLRSHYEA 147
           Q L++ T+TIRH A+ TAVPYRQ+ +F PGTG GGAG HWSG HFR  P +  LRS+ E 
Sbjct: 67  QSLAQDTLTIRHKAADTAVPYRQMGSFKPGTGVGGAGSHWSGCHFRALPEDFRLRSNMEQ 126

Query: 148 RYGKNFIPEGMTIQDFGVSYNELEPFFDQAEKVFGTSGSAWTIKGKMIGKEKGGNFYAPD 207
           RYG+ FIP+ MTIQDF VSY +LEP FD  E V GTSG A  I G +   + GGN +   
Sbjct: 127 RYGRGFIPDDMTIQDFPVSYEDLEPHFDHFEYVCGTSGKAGIINGVL---QPGGNPFEGS 183

Query: 208 RSSDFPLPAQKRTYSAQLFAQAAESVGYHPYDMPSANTSGPYTNTYGAQMGPCNFCGYCS 267
           RS +F LP       A++F +AAE +G+HPY +P++NTS  YTN YG QMGPCN CG+CS
Sbjct: 184 RSREFALPPNPDYLGAEMFYKAAEGMGWHPYPIPASNTSRAYTNPYGCQMGPCNACGFCS 243

Query: 268 GYACYMYSKASPNVNILPALRQEPKFELRNNAYVLRVNLTGDKKRATGVTYLDGQGREVV 327
            Y C  YSKASPN  ILP LRQ   FELR +A VL+VNL    K+ATGVTYLD  GRE+ 
Sbjct: 244 DYGCLNYSKASPNACILPVLRQRDTFELRTHAQVLKVNLDSTGKKATGVTYLDATGREIE 303

Query: 328 QPADLVILSAFQFHNVHLMLLSGIGQPYNPITNEGVVGRNFAYQNISTLKALFDKNTTTN 387
           QPADLV+L AF + NVHLML+SGIG PY+P T  G VG+N++YQN++ +   FDK+   N
Sbjct: 304 QPADLVLLCAFSYINVHLMLVSGIGTPYDPQTGLGTVGKNYSYQNLNRVVLFFDKSVQAN 363

Query: 388 PFIGAGGAGVAVDDFNADNFDHGPYGFVGGSPFWVNQAGTKPVSGLPTPKGTPNWGSQWK 447
            FIG GGAG  +DD N +  D+G  GFVGG   W  Q G  PV G+  P GTP+WGS+WK
Sbjct: 364 GFIGIGGAGATMDDLNGNQLDNGKAGFVGGGLVWARQPGAGPVRGINVPPGTPSWGSKWK 423

Query: 448 AAVADTYNHHISMDAHGAHQSYRANYLDLDPNYKNVYGQPLLRMTFDWQDNDIRMAQFMV 507
            A  D++ H    +  GA  SYR +YL LDP Y++ +G+PLLRMTFDW DN+I+ +QF+V
Sbjct: 424 QAAVDSFRHSFYYEVQGACMSYRQHYLSLDPTYRDAFGRPLLRMTFDWHDNEIKASQFLV 483

Query: 508 GKMRKITEAMNPKMIIGGAKGPGTHFDTTVYQTTHMSGGAIMGEDPKTSAVNRYLQSWDV 567
            K  +++  +NP  + G AK  G+H+D T YQ+TH  GGAIMG  P  SA+NRYLQSWDV
Sbjct: 484 DKALQMSRILNPIAVSGDAKKDGSHYDITKYQSTHTCGGAIMGHTPADSALNRYLQSWDV 543

Query: 568 PNVFVPGASAFPQGLGYNPTGMVAALTYWSAKAIREQYLKNPGPLVQA 615
           PNVF  GA+AFPQ  GYNPTGMV AL YW+AKAIR++YL +PGPLVQA
Sbjct: 544 PNVFAIGANAFPQNNGYNPTGMVGALAYWAAKAIRDKYLADPGPLVQA 591


Lambda     K      H
   0.317    0.135    0.416 

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: 1275
Number of extensions: 63
Number of successful extensions: 2
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: 615
Length of database: 591
Length adjustment: 37
Effective length of query: 578
Effective length of database: 554
Effective search space:   320212
Effective search space used:   320212
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: 41 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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