GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__azobra:AZOBR_RS15015 AZOBR_RS15015
           dihydroxy-acid dehydratase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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