GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Caulobacter crescentus NA1000

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate CCNA_00193 CCNA_00193 3-isopropylmalate dehydrogenase

Query= BRENDA::Q5SIJ1
         (334 letters)



>FitnessBrowser__Caulo:CCNA_00193
          Length = 350

 Score =  213 bits (542), Expect = 6e-60
 Identities = 145/350 (41%), Positives = 197/350 (56%), Gaps = 26/350 (7%)

Query: 5   ICLIEGDGIGHEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVEKILSCHA 64
           + L+ GDGIG EV    RRV  A    L+  EA  G  +++  GT + +E  E+ L+  A
Sbjct: 4   LLLLPGDGIGPEVCAQVRRVAAALTPDLKVDEALYGGASYDTHGTPLTDEVREQALASDA 63

Query: 65  TLFGAATSPT-----RKVPGFFGAIRYLRRRLDLYANVRPA--------KSRPVPGSRPG 111
            L GA   P      R +    G +  LR+ +D++AN+RPA         S   P    G
Sbjct: 64  VLMGAVGGPKWADAPRHLRPEAGLLN-LRKAMDVFANLRPAYCFEALAGASSLKPELVSG 122

Query: 112 VDLVIVRENTEGLYVEQERRYLDVAIADA------VISKKASERIGRAALRIAEGRPRKT 165
           +D++ VRE   G+Y  Q R   D+A          V +    ER+GR A  +A GR  K 
Sbjct: 123 LDIMFVRELVGGVYFGQPRGIEDLADGQKKGFDTQVYTTSEIERVGRVAFELARGRTNK- 181

Query: 166 LHIAHKANVLPLTQGLFLDTVKEV-AKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTN 224
           +H A K+NV+  +  L+   + E+ A+++P V ++ I+ DNCAMQLV  P++FDVIVT N
Sbjct: 182 VHSAEKSNVME-SGLLWKQVITELHAREYPDVQLEHILADNCAMQLVRAPKQFDVIVTDN 240

Query: 225 LLGDILSDLAAGLVGGLGLAPSGNIG--DTTAVFEPVHGSAPDIAGKGIANPTAAILSAA 282
           L GDILSD AA L G LG+ PS  +G      ++EP+HGSAPDIAGKG+ANP AAILS  
Sbjct: 241 LFGDILSDAAAMLTGSLGMLPSAALGAPGKPGLYEPIHGSAPDIAGKGLANPLAAILSFE 300

Query: 283 MMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331
           M L + L + EAA  +  AV   L+ G RT DLGG  TT    +AV+ AL
Sbjct: 301 MALRWSLKQTEAADALLAAVKAALDNGARTRDLGGSLTTTQMGDAVLAAL 350


Lambda     K      H
   0.319    0.137    0.391 

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: 300
Number of extensions: 20
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: 334
Length of database: 350
Length adjustment: 29
Effective length of query: 305
Effective length of database: 321
Effective search space:    97905
Effective search space used:    97905
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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