GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysU in Caulobacter crescentus NA1000

Align Homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate CCNA_03781 CCNA_03781 aconitate hydratase

Query= SwissProt::Q9ZND9
         (163 letters)



>FitnessBrowser__Caulo:CCNA_03781
          Length = 895

 Score = 53.5 bits (127), Expect = 9e-12
 Identities = 40/117 (34%), Positives = 62/117 (52%), Gaps = 12/117 (10%)

Query: 13  TDDILPGKYAPFMVGEDRFHLYAFAHLRPEFAKEVRPGDILVFGRNAGLGSSREYAPEAL 72
           T DI  G    F  GE    + +      ++ +E RP  ++  G+  G GSSR++A +  
Sbjct: 733 TPDIEGGVTKHFPTGE----VMSIYDAAMKYQEEGRPA-VVFGGKEYGTGSSRDWAAKGT 787

Query: 73  KRLGVRAIIAKSYARIFFRNLVNLGIVPFESEEVVDALEDG-DEVELDLESGVLTRG 128
           K LGVRA+I +S+ RI   NLV +G++P +       ++DG  ++EL  E  V  RG
Sbjct: 788 KLLGVRAVICESFERIHRSNLVGMGVLPLQ------FVQDGWQKLELTGEEIVSIRG 838


Lambda     K      H
   0.322    0.144    0.432 

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: 289
Number of extensions: 13
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 163
Length of database: 895
Length adjustment: 30
Effective length of query: 133
Effective length of database: 865
Effective search space:   115045
Effective search space used:   115045
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 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