GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Sphingobium czechense LL01

Align phosphogluconate dehydratase (characterized)
to candidate WP_066605615.1 V473_RS11950 dihydroxy-acid dehydratase family protein

Query= CharProtDB::CH_024239
         (603 letters)



>NCBI__GCF_001046645.1:WP_066605615.1
          Length = 600

 Score =  175 bits (443), Expect = 6e-48
 Identities = 144/458 (31%), Positives = 217/458 (47%), Gaps = 49/458 (10%)

Query: 136 AAVGLSHNMF----DGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLPNKEKV 191
           A +GL   M+    DG +    CDK  P L MAA +  ++PA+ +  GPM +G    E+ 
Sbjct: 108 AYLGLVEAMYGYPLDGVILTTGCDKTTPALLMAAATV-NIPAIALSVGPMLNGWFKGERT 166

Query: 192 -------RIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQLPGS 244
                  + R+L A GK+D    ++  A+S  + G C   GTA+T   + E +GM LPGS
Sbjct: 167 GSGTIVWKGRELLAAGKIDDEGFIKLVASSAPSTGYCNTMGTASTMNSLAEALGMMLPGS 226

Query: 245 SFVHPDSPLRDALTAA--AARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGSTN 302
           + +   +P RD    A    +++  M     E +    ++      N IV   A GGSTN
Sbjct: 227 AAI--PAPYRDRQEVAYLTGKRIVDMVA---EDLKPSDIMTLDAFHNAIVVNSAIGGSTN 281

Query: 303 HTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRELLK 362
             +HL A+AR  G+ +   D+  +   VPL+  L P G      +  AGGVP +V +L+ 
Sbjct: 282 APIHLSAIARHMGVDLPLKDWETVGHKVPLLVNLQPAGEYLGEDYYRAGGVPAVVSQLID 341

Query: 363 AGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGTKV 422
            GL+     TV G      T+       E++         D  VI  F+QP     G  V
Sbjct: 342 QGLIRTSAMTVNG-----KTMGENCKGVEIE---------DEKVIRPFDQPLVTDAGFLV 387

Query: 423 LSGNL-GRAVMKTSAVPVE-----------NQVIEAPAVVFESQHDVMPAFE--AGLLDR 468
           LSGNL   AVMKTS + VE            +  E PAVVF+   D     +  A  +  
Sbjct: 388 LSGNLFDAAVMKTSVISVEFRDRYLSNPDDPEAFEGPAVVFDGPEDYHHRIDDPATGITA 447

Query: 469 DCVVVVRHQGPKA-NGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTP 527
           + ++ +R  GP    G  E+  + PP  ++ +    +  + DGR SG SG  PS ++ +P
Sbjct: 448 NSLMFMRGAGPIGYPGAAEVVNMRPPAYLITEGVSALPCIGDGRQSGTSGS-PSILNASP 506

Query: 528 EAYDGGLLAKVRDGDIIRVNGQTGELTLLVDEAELAAR 565
           EA   G LA +  GD +R++ + G + +L+ + ELA R
Sbjct: 507 EAAAMGGLALLETGDRVRMDLKAGTVNVLISDEELAER 544


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: 847
Number of extensions: 55
Number of successful extensions: 7
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: 600
Length adjustment: 37
Effective length of query: 566
Effective length of database: 563
Effective search space:   318658
Effective search space used:   318658
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