GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Caulobacter crescentus NA1000

Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate CCNA_03491 CCNA_03491 gluconate 5-dehydrogenase (Ga5DH)-related protein

Query= metacyc::MONOMER-11802
         (255 letters)



>FitnessBrowser__Caulo:CCNA_03491
          Length = 260

 Score =  100 bits (248), Expect = 4e-26
 Identities = 79/256 (30%), Positives = 125/256 (48%), Gaps = 16/256 (6%)

Query: 2   HIANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQ---AVEAKARELGDNARFAVA 58
           +++ K  +V+G   G+G   A+ + +AGA +++   N +   A E     LG   +    
Sbjct: 7   NLSGKVALVTGGNRGIGLGMAKAMAQAGADIVIWGSNPERNLAAEQTLTALGVRVKAQTV 66

Query: 59  DISDEQAAQSAVDAAVSAFGSLHGLVNCAGI-VGAEKVLGKQGPHGLASFAKVINVNLIG 117
           D+SDE   +  ++ AV+A G +  +   AGI  G+   +          + KV+ VNL G
Sbjct: 67  DVSDEAQVREGMEEAVAAMGRVDSVFANAGIGYGSPSFVDMS----TEVYRKVLAVNLDG 122

Query: 118 SFNLLRLAAAAMAEGA-ADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAA 176
            F  LR A   M E A A + G  G ++  AS+AA +G     AYAA+KGA+ S+    A
Sbjct: 123 VFFTLREACRHMVERAKAGDPG--GSLVGVASLAAIEGAARNEAYAATKGAVISMIKSVA 180

Query: 177 RELARFGIRVMTIAPGIFETPMMAGMSDEVRASLAAGVPFPP--RLGRPQEYAALARHII 234
            E AR+G+R   I PG   T M AG      A     +P  P  R G P+++  +A ++ 
Sbjct: 181 VEHARYGVRANAILPGWIATDMTAGAQGNA-AFAEKVIPRVPARRWGEPEDFGGMAVYLA 239

Query: 235 E--NSMLNGEVIRLDG 248
              +S  +G  + +DG
Sbjct: 240 SDASSYHSGTTLVIDG 255


Lambda     K      H
   0.318    0.131    0.358 

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: 120
Number of extensions: 3
Number of successful extensions: 3
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: 255
Length of database: 260
Length adjustment: 24
Effective length of query: 231
Effective length of database: 236
Effective search space:    54516
Effective search space used:    54516
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: 47 (22.7 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