GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Acidovorax sp. GW101-3H11

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 Ac3H11_955 Dihydroxy-acid dehydratase (EC 4.2.1.9)

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_955
          Length = 619

 Score =  253 bits (645), Expect = 2e-71
 Identities = 191/591 (32%), Positives = 288/591 (48%), Gaps = 73/591 (12%)

Query: 44  RPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASEN-TFRPTAMMY- 101
           +P+I ++N+++   P + HL++L + V   +  AGG   E    +  +        M+Y 
Sbjct: 34  KPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYS 93

Query: 102 ---RNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYF 158
              R++ A +VE  +     D  V +  CDK TP +LM A   ++P I V+GGPM  G  
Sbjct: 94  LPSRDIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPVIFVSGGPMEAGKT 153

Query: 159 RGERVGSGTHLWKFSEMVKA------GEMTQAEFLEAEASMSRSSGTCNTMGTASTMASM 212
           R     +    +K  ++V A         + A+  E E S   + G+C+ M TA++M  +
Sbjct: 154 RLANPVTKVMEFKKLDLVDAMVIAADSNYSDADVAEVERSACPTCGSCSGMFTANSMNCL 213

Query: 213 AEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVK-----DDLK--PSEIMTKQAFEN 265
            EALG++L GN  +    + R+ + +  GRRIV + K     DD +  P  +  K AFEN
Sbjct: 214 TEALGLSLPGNGTVVATHADREQLFKRAGRRIVDLAKQYYEQDDERVLPRSVGFK-AFEN 272

Query: 266 AIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMP-SGKYLMEEFF 324
           A+  + A+GGSTN ++HLLAIA    I  ++ D DR  R VP +  + P + KY +E+  
Sbjct: 273 AMTLDIAMGGSTNTILHLLAIASEAEIPFTMADIDRLSRVVPQLCKVAPNTNKYHIEDVH 332

Query: 325 YAGGLPVVLKRLGEAGLLHKDALTVSGETV------WDEVK------------------- 359
            AGG+  +L  L  AG LH D  TV   T+      WD V+                   
Sbjct: 333 RAGGIMAILGELDRAGKLHTDVPTVHTATLKDALDQWDIVRTQDEAVRTFYMAGPAGVPT 392

Query: 360 -----DVVNW-------NEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLV 407
                    W        E  I   + A +  GG+ VL GN+A  G V+K +     +LV
Sbjct: 393 QVAFSQATRWPSLDLDRAEGCIRSYDHAFSKEGGLAVLTGNIAVDGCVVKSAGVDESILV 452

Query: 408 HKGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLK-K 466
            +G A V E  D+  A I  D +   +  +++++  GPKG PGM E   M  P   +K K
Sbjct: 453 FEGTAHVTESQDEAVANILADKVQAGD--VVIVRYEGPKGGPGMQE---MLYPTSYIKSK 507

Query: 467 GI-LDMVRISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISD 525
           G+      ++D R SG   G  + H SPEAA GG + +V+NGD I +D+PNR +++ +SD
Sbjct: 508 GLGKACALLTDGRFSGGTSGLSIGHCSPEAAAGGAIGLVQNGDRIRIDIPNRTINVLVSD 567

Query: 526 EELARR-----LAEWQPNHDLPTSGYAFL--HQQHVEGADTGA--DLDFLK 567
           EELA+R        W+P    P    A L  + + V  AD GA  DL  L+
Sbjct: 568 EELAKRREAQNAKGWKPAQPRPRKVSAALKAYAKLVMSADKGAVRDLSLLE 618


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: 928
Number of extensions: 48
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 579
Length of database: 619
Length adjustment: 37
Effective length of query: 542
Effective length of database: 582
Effective search space:   315444
Effective search space used:   315444
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