GapMind for catabolism of small carbon sources

 

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

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate Ac3H11_955 Dihydroxy-acid dehydratase (EC 4.2.1.9)

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_955
          Length = 619

 Score =  209 bits (531), Expect = 4e-58
 Identities = 181/595 (30%), Positives = 274/595 (46%), Gaps = 68/595 (11%)

Query: 68  VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127
           +A+V+S+   +  H   +   + + + +   G V +    T A+ DG+  G  GM  SLP
Sbjct: 37  IAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAK-EFNTIAVDDGIAMGHDGMLYSLP 95

Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG--- 184
           SR++IA S    ++ +  DA + +  CDKI PG++M A+R  ++P IFV GGPM +G   
Sbjct: 96  SRDIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRL-NIPVIFVSGGPMEAGKTR 154

Query: 185 ----------ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLM 234
                         +  D     A+   +  ++ E E  +  + G+C+   TAN+   L 
Sbjct: 155 LANPVTKVMEFKKLDLVDAMVIAADSNYSDADVAEVERSACPTCGSCSGMFTANSMNCLT 214

Query: 235 EVMGLHLPGASFVNPYTPLRDALTHEAAQQVTRLTKQ---SGNFTPIGEIVDERSLVNSI 291
           E +GL LPG   V      R+ L   A +++  L KQ     +   +   V  ++  N++
Sbjct: 215 EALGLSLPGNGTVVATHADREQLFKRAGRRIVDLAKQYYEQDDERVLPRSVGFKAFENAM 274

Query: 292 VALHATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAA 350
               A GGSTN  LH+ AIA  A I  T  D+  LS VVP L  V PN  K  I     A
Sbjct: 275 TLDIAMGGSTNTILHLLAIASEAEIPFTMADIDRLSRVVPQLCKVAPNTNKYHIEDVHRA 334

Query: 351 GGMAFLIRELLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLV----------WRDGPI- 399
           GG+  ++ EL  AG LH DV TV        T +  LD   +V          +  GP  
Sbjct: 335 GGIMAILGELDRAGKLHTDVPTV-----HTATLKDALDQWDIVRTQDEAVRTFYMAGPAG 389

Query: 400 -------------ESLD----ENILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQ 440
                         SLD    E  +R    AFS EGGL V+ GN+     V+K + V   
Sbjct: 390 VPTQVAFSQATRWPSLDLDRAEGCIRSYDHAFSKEGGLAVLTGNIAVDGCVVKSAGVDES 449

Query: 441 HQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQD 499
             + E  A V + Q +      A +++   V ++R++GP+   GM E+   T ++   + 
Sbjct: 450 ILVFEGTAHVTESQDEAVANILADKVQAGDVVIVRYEGPKGGPGMQEMLYPTSYI-KSKG 508

Query: 500 RGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDA 559
            G   AL+TDGR SG +  +    H SPEA  GGA+  V++GD IR+D    T+ + V  
Sbjct: 509 LGKACALLTDGRFSGGTSGLSIG-HCSPEAAAGGAIGLVQNGDRIRIDIPNRTINVLVSD 567

Query: 560 DEFAAREPAKGLLG--------NNVGSGRELFGFMRMAFSSAEQGASAFTSALEN 606
           +E A R  A+   G          V +  + +  + M   SA++GA    S LE+
Sbjct: 568 EELAKRREAQNAKGWKPAQPRPRKVSAALKAYAKLVM---SADKGAVRDLSLLED 619


Lambda     K      H
   0.318    0.134    0.386 

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: 869
Number of extensions: 50
Number of successful extensions: 9
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: 608
Length of database: 619
Length adjustment: 37
Effective length of query: 571
Effective length of database: 582
Effective search space:   332322
Effective search space used:   332322
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