GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Dyella japonica UNC79MFTsu3.2

Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate N515DRAFT_0569 N515DRAFT_0569 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0569
          Length = 568

 Score =  273 bits (697), Expect = 2e-77
 Identities = 172/526 (32%), Positives = 280/526 (53%), Gaps = 18/526 (3%)

Query: 44  RPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPT-----A 98
           +P++ +++TWS+++PCN +LRELAE+V  G+  AGG P+E    + ++     T     +
Sbjct: 31  KPLVAVVHTWSNVSPCNLNLRELAEQVAEGIRAAGGTPIEFNTIAVTDGIAMGTPGMRAS 90

Query: 99  MMYRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYF 158
           ++ R +   ++E A+ G  +D  V+L GCDKT P+  M  A  D+P++ + GG + +G  
Sbjct: 91  LISREVITDSIELAVDGHCLDAMVVLCGCDKTIPAAAMAMARLDIPAVALYGGTIAHGTH 150

Query: 159 RGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGM 218
               + +   +++      AG++  AE    E      +G C    TA+TMA +   LG+
Sbjct: 151 DAHPI-TIQQVFEAVGAHGAGKIDDAELAAVERDACPGAGACGGQFTANTMAMVLTTLGL 209

Query: 219 ALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTN 278
           +  G   IP     +   A+  G  ++  +++   P  ++ + +  NA R  AA  GSTN
Sbjct: 210 SPMGFNDIPATHPAKAAAARRCGELVMDCLREQRTPRALINRTSLRNAARMVAATAGSTN 269

Query: 279 AVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGE 338
           AV+HLLAIA   G   +L+D++   +  P I +L+P G+Y   E F AGG   V + L  
Sbjct: 270 AVLHLLAIAREAGAPWTLEDFEPASKHTPVIADLLPGGRYTAVEMFGAGGAARVAQELIA 329

Query: 339 AGLLHKDALTVSGETVWDEVKDVVN-WNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLK 397
           AG+L  D  TV+G ++++E         +DVILP  + L   GG  +L GNLAP+G +LK
Sbjct: 330 AGML-DDVPTVTGRSLFEEAAAAPRAEQQDVILPVGQPLKPRGGYSILYGNLAPEGCILK 388

Query: 398 PSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNM 457
              A       +G A VFE  +   A +      I +  ++V++N GP G PGM E+  +
Sbjct: 389 --LAGKGATHFEGTARVFESEEQAFAAVQQGR--IAKGDVIVIRNEGPAGGPGMREM--L 442

Query: 458 GLPPKVLKKGILDMVR-ISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPN 516
           G+   ++ +G+ D V  I+D R SG  +G +V H +PEA  GGP+A++++GD I +D   
Sbjct: 443 GVTAALIGRGLGDDVALITDGRFSGATHGFMVGHMAPEAVRGGPIALLRDGDRIRIDAGL 502

Query: 517 RRLHLDISDEELARRLAEWQPNHDLPTSGYAFLHQQHVEGADTGAD 562
           R +    +D +LA R   W P     T+G    + + V  A  GA+
Sbjct: 503 REI---ATDADLAERRQHWTPPAPKVTTGALAKYARLVGSASDGAN 545


Lambda     K      H
   0.318    0.135    0.408 

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: 842
Number of extensions: 41
Number of successful extensions: 7
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: 579
Length of database: 568
Length adjustment: 36
Effective length of query: 543
Effective length of database: 532
Effective search space:   288876
Effective search space used:   288876
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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