GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Rhodobacter ovatus JA234

Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate WP_097030654.1 CRO07_RS10535 c-type cytochrome

Query= BRENDA::Q5FRK5
         (437 letters)



>NCBI__GCF_900207575.1:WP_097030654.1
          Length = 547

 Score =  156 bits (394), Expect = 2e-42
 Identities = 101/284 (35%), Positives = 141/284 (49%), Gaps = 18/284 (6%)

Query: 23  DSDKAIVEKGRYLAAASDCAACHSVHGKPEYS---GGVSFSLPMGKIYSTNITPDPDHGI 79
           D+  A ++ G+ +  A DCA CH+  G+P+ +   GG       G+ +  NI+PD   GI
Sbjct: 47  DAGPADLDNGQRIFLAGDCATCHATPGQPDQTKLGGGRVLDTAFGRFHMPNISPDRVDGI 106

Query: 80  GRYTEAQFGQALRQG-----IRRDGSTLYPAMPFPSYARLTDSDIHALFVYFRDGVKAVP 134
           G +T  QF +A+R+G     I  DG  LYP+ P+ SY RL  +D+  ++ Y    +  V 
Sbjct: 107 GGWTLEQFTRAVREGVGPGGIMPDGQNLYPSFPYTSYQRLNANDVRDMYAYIMS-LPPVA 165

Query: 135 VSAPRNEIPWPLSIRWPLTFWRWAFA---PTPHKAITSTAGEFTDPLLARGAYLVEGPAH 191
              P +E+ +P +IR  +  WR AF    P P    T TA +    +LARG YLVEG  H
Sbjct: 166 GQVPGHELKFPYNIRRGIGVWRLAFLDGQPLPDAPATQTAPDPHQAVLARGRYLVEGAGH 225

Query: 192 CGACHSPRAITMQEKALIAHDGSLYLAGGAPVDGWTPPSLRQENRTGLGRWSEEDIVSFL 251
           C  CHSPR+      A      S Y  GG   DG         + TG+G WS   I ++L
Sbjct: 226 CAECHSPRSFMGNVIA-----DSRY-GGGPTPDGHGHFPNISPDETGIGFWSVNAIANYL 279

Query: 252 RTGRSNPGSVFGSMTSAVLHGTQKLTDNDLHAIAHYLKSLPPAD 295
            TG S  G   G     V+  T +L   D  A+A YLK++P  D
Sbjct: 280 ETGISPIGKKAGGDMEEVILNTAQLPREDRLAMAMYLKTVPAVD 323



 Score = 41.6 bits (96), Expect = 6e-08
 Identities = 46/140 (32%), Positives = 61/140 (43%), Gaps = 19/140 (13%)

Query: 17  AEATAQDSDKAIVEKGRYLA-AASDCAACHS-------VHGKPEYSGGVSFSLPMGKIYS 68
           A  TA D  +A++ +GRYL   A  CA CHS       V     Y GG +   P G  + 
Sbjct: 201 ATQTAPDPHQAVLARGRYLVEGAGHCAECHSPRSFMGNVIADSRYGGGPT---PDGHGHF 257

Query: 69  TNITPDPDHGIGRYTEAQFGQALRQGIRRDGSTLYPAMP--FPSYARLTDSDIHALFVYF 126
            NI+PD + GIG ++       L  GI   G      M     + A+L   D  A+ +Y 
Sbjct: 258 PNISPD-ETGIGFWSVNAIANYLETGISPIGKKAGGDMEEVILNTAQLPREDRLAMAMY- 315

Query: 127 RDGVKAVP-VSAPRNEIPWP 145
              +K VP V AP    P P
Sbjct: 316 ---LKTVPAVDAPGPGRPEP 332


Lambda     K      H
   0.319    0.133    0.420 

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: 787
Number of extensions: 52
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 437
Length of database: 547
Length adjustment: 34
Effective length of query: 403
Effective length of database: 513
Effective search space:   206739
Effective search space used:   206739
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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:

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:

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:

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:

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