GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Azospirillum brasilense Sp245

Align phosphogluconate dehydratase (characterized)
to candidate AZOBR_RS31260 AZOBR_RS31260 dihydroxy-acid dehydratase

Query= CharProtDB::CH_024239
         (603 letters)



>FitnessBrowser__azobra:AZOBR_RS31260
          Length = 608

 Score =  184 bits (466), Expect = 1e-50
 Identities = 138/442 (31%), Positives = 209/442 (47%), Gaps = 41/442 (9%)

Query: 146 DGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLPNKEKV-------RIRQLYA 198
           DG +    CDK  P   MAA +  ++PA+ +  GPM +G    E+        + RQ+ A
Sbjct: 130 DGVVLTIGCDKTTPACLMAAATV-NIPAIALSVGPMLNGWFRGERTGSGTIVWKARQMMA 188

Query: 199 EGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQLPGSSFVHPDSPLRDALT 258
            G++D    +E  A+S  + G C   GTA+T   + E +GMQLPGS+ +      R    
Sbjct: 189 AGEIDYQGFIELVASSAPSTGYCNTMGTASTMNSLAEVLGMQLPGSAAIPAPYRERQQAD 248

Query: 259 AAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGSTNHTMHLVAMARAAGIQI 318
               +++  M     E +    ++     +N IV   A GGSTN  +H+ A+A+  G+ +
Sbjct: 249 YETGKRIVEMV---REDLKPSDILTRDAFLNAIVVNSAIGGSTNAPIHINAIAKHIGVPL 305

Query: 319 NWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRELLKAGLLHEDVNTVAGFGL 378
             +D+      VPL+  L P G      F  AGGVP +V +L+  GL+ E   TV G  +
Sbjct: 306 TVEDWQTHGHDVPLLVNLQPAGEYLGEDFHRAGGVPAVVAQLMGKGLIREGAPTVNGRTI 365

Query: 379 SRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGTKVLSGNL-GRAVMKTSAV 437
                      GE   R   +  LD+ VI   ++P   + G  VL GNL G A+MKTS +
Sbjct: 366 -----------GENCRR---QPILDTRVIHPIDEPLMPNAGFVVLRGNLFGAAIMKTSVI 411

Query: 438 -----------PVENQVIEAPAVVFESQHDVMPAFEAGLLDRDC--VVVVRHQGPKA-NG 483
                      P + +  E   VVF+   D     +   L  D   ++V+R  GP    G
Sbjct: 412 SDEFRERYLSNPQDPEAFEGKVVVFDGPEDYHHRIDDPSLGIDAYTILVIRGTGPIGYPG 471

Query: 484 MPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRDGDI 543
             E+  + PP  ++      +  + DGR SG SG  PS ++ +PEA  GG LA +R GD 
Sbjct: 472 AAEVVNMRPPATLIKQGVHSLPCIGDGRQSGTSGS-PSILNASPEAAAGGGLALLRSGDR 530

Query: 544 IRVNGQTGELTLLVDEAELAAR 565
           +R++ + G   +L+ E ELA R
Sbjct: 531 VRIDLRRGSADILIPEGELADR 552


Lambda     K      H
   0.318    0.134    0.392 

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: 886
Number of extensions: 53
Number of successful extensions: 6
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: 603
Length of database: 608
Length adjustment: 37
Effective length of query: 566
Effective length of database: 571
Effective search space:   323186
Effective search space used:   323186
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