GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Brucella inopinata BO1

Align phosphogluconate dehydratase (characterized)
to candidate WP_002968570.1 BIBO1_RS18925 dihydroxy-acid dehydratase family protein

Query= CharProtDB::CH_024239
         (603 letters)



>NCBI__GCF_000182725.1:WP_002968570.1
          Length = 601

 Score =  189 bits (480), Expect = 3e-52
 Identities = 143/447 (31%), Positives = 217/447 (48%), Gaps = 51/447 (11%)

Query: 146 DGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLPNKEKV-------RIRQLYA 198
           DG +    CDK  P   MAA +  ++PA+ +  GPM +G    E+        + R+L A
Sbjct: 123 DGVVLTIGCDKTTPACLMAAATV-NIPAIALSVGPMLNGWFRGERTGSGTIVWKARELLA 181

Query: 199 EGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQLPGSSFVHPDSPLRDALT 258
           +G++D    ++  A+S  + G C   GTA T   + E +GMQLPGS+ +   +P RD   
Sbjct: 182 KGEIDYQGFVKLVASSAPSTGYCNTMGTATTMNSLAEALGMQLPGSAAI--PAPYRDRQE 239

Query: 259 AA--AARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGSTNHTMHLVAMARAAGI 316
            A    R++  M    +E +    ++ ++  +N I    A GGSTN  +HL A+AR  G+
Sbjct: 240 VAYLTGRRIVEMV---HEDLKPSDILTKEAFINAIRVNSAIGGSTNAPIHLNALARHIGV 296

Query: 317 QINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRELLKAGLLHEDVNTVAGF 376
           ++  DD+    + +PL+  L P G      +  AGGVP +V +L+  GL+HED  TV G 
Sbjct: 297 ELTVDDWQKYGEEIPLLVNLQPAGEYLGEDYYHAGGVPAVVNQLMGQGLIHEDAITVNG- 355

Query: 377 GLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGTKVLSGNL-GRAVMKTS 435
                T+     N  ++         D NVI +++QP   H G +VL GNL   A+MK S
Sbjct: 356 ----KTIGENCKNATIE---------DGNVIKTYDQPLKKHAGFRVLRGNLFSSAIMKLS 402

Query: 436 AVPVE-----------NQVIEAPAVVFESQHDVM-----PAFEAGLLDRDCVVVVRHQGP 479
            +  E               E  AVVF+   D       PA E   +D   V+ +R  GP
Sbjct: 403 VISDEFRNRYLSDAKDPNAFEGKAVVFDGPEDYHHRIDDPALE---IDEHTVLFMRGAGP 459

Query: 480 KA-NGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKV 538
               G  E+  +  P  +L      +  + DGR SG SG  PS ++ +PEA  GG LA +
Sbjct: 460 IGYPGAAEVVNMRAPDYLLKKGITSLPCIGDGRQSGTSGS-PSILNASPEAAAGGGLAIL 518

Query: 539 RDGDIIRVNGQTGELTLLVDEAELAAR 565
           + GD +R++   G   +L+ + ELA R
Sbjct: 519 KTGDRVRIDLGRGTADILISDEELAER 545


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: 848
Number of extensions: 40
Number of successful extensions: 5
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: 601
Length adjustment: 37
Effective length of query: 566
Effective length of database: 564
Effective search space:   319224
Effective search space used:   319224
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 24 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