GapMind for Amino acid biosynthesis

 

Alignments for a candidate for preph-dehydratase in Caulobacter crescentus NA1000

Align prephenate dehydratase (EC 4.2.1.51) (characterized)
to candidate CCNA_03028 CCNA_03028 prephenate dehydratase

Query= BRENDA::Q5NLV8
         (337 letters)



>FitnessBrowser__Caulo:CCNA_03028
          Length = 283

 Score =  221 bits (562), Expect = 2e-62
 Identities = 131/279 (46%), Positives = 171/279 (61%), Gaps = 8/279 (2%)

Query: 54  LSPTKAVAFQGAPGCNSNIAIQDLFPDSLPLPCFSFADALTAVKEGRAGRAMIPIENSLN 113
           +S  K +AFQG PG NS+ A +  FPD    PC +F +A  A+K G A   MIPIENS+ 
Sbjct: 1   MSLLKKIAFQGEPGANSHEACRTYFPDYEAYPCKTFEEAFEAIKSGVAQLGMIPIENSIA 60

Query: 114 GRVADMHFLLPESGLTIQAEYFLPINHCLVAPKGA--GEITHVLSHPQALGQCRHWLQAH 171
           GRVAD+H LLP SGL I  E F PI   L+A KG    +I  V S P AL QCR+ L+  
Sbjct: 61  GRVADVHHLLPASGLKIIGERFKPIRFQLMANKGVKLEDIKVVSSMPIALSQCRNSLKRL 120

Query: 172 NLRALAHADTAGAAAEVADRKQAGLAALSPALAAKLYGLEILEKGIADGDTNITRFVVLA 231
            +   A  DTAGAA  +A +     AA++PALAA++YGL+IL + I D   N TRF+V+ 
Sbjct: 121 GVETEAAGDTAGAAKALALKPNPTHAAVAPALAAEIYGLDILARDIEDERHNTTRFLVMT 180

Query: 232 EADTALQDLPPIRQNLSGKMMTSLLFTVKNTPSALLNAIKGFGDNQVNMTKLESYQHGAS 291
                  D  P   + + + +TS +F V+N P+AL  A+ GF  N VNMTKLESY  G +
Sbjct: 181 ------ADKAPAAPDFTHRCVTSFVFRVRNLPAALYKALGGFATNGVNMTKLESYMEGGN 234

Query: 292 FSATQFYADVEGEPSEDNVARALDILQENACDLRILGVY 330
           F+AT FYA+V+G P + N+A ALD L+  +    ILGVY
Sbjct: 235 FTATFFYAEVDGRPEDRNLALALDELKFFSERFEILGVY 273


Lambda     K      H
   0.318    0.132    0.382 

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: 215
Number of extensions: 8
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: 337
Length of database: 283
Length adjustment: 27
Effective length of query: 310
Effective length of database: 256
Effective search space:    79360
Effective search space used:    79360
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: 48 (23.1 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