GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Caulobacter crescentus NA1000

Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate CCNA_01563 CCNA_01563 2-dehydro-3-deoxygluconokinase

Query= BRENDA::Q9WXS2
         (339 letters)



>FitnessBrowser__Caulo:CCNA_01563
          Length = 368

 Score =  203 bits (517), Expect = 5e-57
 Identities = 135/343 (39%), Positives = 179/343 (52%), Gaps = 17/343 (4%)

Query: 5   TFGEIMLRLSPPDHKRIFQTDSFDVTYGGAEANVA-AFLAQMGLDAYFVTKLPNNPLGDA 63
           +FGE+MLR  P    R+     F V  GG E NVA AF    G  +  VT LP N LG  
Sbjct: 20  SFGEVMLRFDP-GFGRVRNARQFQVWEGGGEYNVARAFKKCWGKRSTAVTALPVNDLGWL 78

Query: 64  AAGHLRKFGVKTDYI------ARGGN-RIGIYFLEIGASQRPSKVVYDRAHSAISEAKRE 116
               + + GV T +I        G N R+G+ F E G   RP+    DR HSA S+ +  
Sbjct: 79  VEDLMMQGGVDTSHIIWRDFDGLGRNTRVGLNFTEKGFGVRPALGCSDRGHSAASQIRPG 138

Query: 117 DFDWEKIL--DGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWT- 173
           + +WEK+   +G RWFH  GI   L       + +A++VA + G  VS DLNYRA LW  
Sbjct: 139 EVNWEKLFGEEGVRWFHTGGIFAALASNTAEAVIEAVEVARKYGTVVSYDLNYRASLWKS 198

Query: 174 ---KEEAQKVMIPFMEYVDVLIANEEDIEKVLGISVEGLDLKTGKLNREAYAKIAEEVTR 230
              KE AQKV     +YVDV+I NEED    LG  VEGLD     ++   + K+ E   +
Sbjct: 199 QGGKEGAQKVNRHIAQYVDVMIGNEEDFTACLGFEVEGLDEHISSIDPANFKKMIETAVK 258

Query: 231 KY-NFKTVGITLRESISATVNYWSVMVFENGQPHFSN-RYEIHIVDRVGAGDSFAGALIY 288
           ++ NFK    TLR + +A+VN WS +++  GQ + S  R  + I DRVG GD FA  L Y
Sbjct: 259 QFPNFKVAATTLRNAKTASVNDWSAILYAGGQFYASMMRENLEIYDRVGGGDGFASGLAY 318

Query: 289 GSLMGFDSQKKAEFAAAASCLKHTIPGDFVVLSIEEIEKLASG 331
           G + G   Q   E+ AA   L  T PGD  ++  EE+E +  G
Sbjct: 319 GFMEGKGPQAAVEYGAAHGALAMTTPGDTSMVRKEEVEAVMKG 361


Lambda     K      H
   0.319    0.136    0.397 

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: 311
Number of extensions: 21
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: 339
Length of database: 368
Length adjustment: 29
Effective length of query: 310
Effective length of database: 339
Effective search space:   105090
Effective search space used:   105090
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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