GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Azospirillum brasilense Sp245

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 AZOBR_RS15015 AZOBR_RS15015 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__azobra:AZOBR_RS15015
          Length = 621

 Score =  242 bits (617), Expect = 4e-68
 Identities = 181/545 (33%), Positives = 268/545 (49%), Gaps = 65/545 (11%)

Query: 43  GRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASEN-TFRPTAMMY 101
           G+P+I I N+++   P + HL++L + V   + +AGG   E    +  +        M+Y
Sbjct: 33  GKPIIAIANSFTQFVPGHVHLKDLGQLVAREIEKAGGVAKEFNTIAVDDGIAMGHDGMLY 92

Query: 102 ----RNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGY 157
               R L A AVE  +     D  V +  CDK TP +LM A   ++P++ V+GGPM  G 
Sbjct: 93  SLPSRELIADAVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPAVFVSGGPMEAGK 152

Query: 158 FRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSS----GTCNTMGTASTMASMA 213
                      L     MV A + T ++  E  A M R S    G+C+ M TA++M  + 
Sbjct: 153 VNWRGKTKAVDL--IDAMVAAADPTVSD--EEAAVMERGSCPTCGSCSGMFTANSMNCLT 208

Query: 214 EALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVK-----DDLK--PSEIMTKQAFENA 266
           EALG++L GN  I    + RK +    GR  V++ +     +D    P  I T +AFENA
Sbjct: 209 EALGLSLPGNGTILATHADRKELFLAAGRMAVELCRRWYQEEDATALPRGIATFEAFENA 268

Query: 267 IRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPS-GKYLMEEFFY 325
           +  + A+GGSTN V+HLLA A    +  ++ D DR  R VP +  + P+     +E+   
Sbjct: 269 MTLDIAMGGSTNTVLHLLAAAQEGQVPFTMADIDRLSRRVPNVCKVAPAVSDVHIEDVHK 328

Query: 326 AGGLPVVLKRLGEAGLLHKDALTVSGETVWD-----EVKDVVN----------------- 363
           AGG+  +L  L   GLL++D  TV  +T+ D     +VK   +                 
Sbjct: 329 AGGIFGILGELDRGGLLNRDVATVHAKTLGDALDRWDVKRTQDEGVHTMFKAAPGGIPTT 388

Query: 364 --------WNE-------DVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVH 408
                   W E        VI   + A +  GG+ VL GN+A KG ++K +      LV 
Sbjct: 389 IAFSQEKRWPELDLDRDKGVIRSVDSAFSKDGGLAVLFGNIAEKGCIVKTAGVDASNLVF 448

Query: 409 KGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLK-KG 467
            G A VFE  D     I  D +   +  ++V++  GP+G PGM E   M  P   LK KG
Sbjct: 449 AGPARVFESQDAAVEAILGDTVKAGD--VVVIRYEGPRGGPGMQE---MLYPTSYLKSKG 503

Query: 468 I-LDMVRISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDE 526
           +      ++D R SG   G  + H SPEAA GG + +V++GD IE+D+PNR+++L +SDE
Sbjct: 504 LGKACALVTDGRFSGGTSGLSIGHASPEAAQGGAIGLVQDGDRIEIDIPNRKINLALSDE 563

Query: 527 ELARR 531
           EL RR
Sbjct: 564 ELQRR 568


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: 46
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: 621
Length adjustment: 37
Effective length of query: 542
Effective length of database: 584
Effective search space:   316528
Effective search space used:   316528
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