GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysU in Klebsiella michiganensis M5al

Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate BWI76_RS04665 BWI76_RS04665 3-isopropylmalate dehydratase small subunit

Query= SwissProt::Q58667
         (170 letters)



>FitnessBrowser__Koxy:BWI76_RS04665
          Length = 201

 Score = 72.0 bits (175), Expect = 6e-18
 Identities = 53/148 (35%), Positives = 75/148 (50%), Gaps = 24/148 (16%)

Query: 13  DVDTDAIIPGPYLRTTDPYELASHCMAGI---DE-----------NFPKKVKEGDVIVAG 58
           +VDTDAIIP  +L+        +H        D+           NFP+  K   +++A 
Sbjct: 19  NVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFQDDKGEQPNPEFVLNFPE-YKGASILLAR 77

Query: 59  ENFGCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPII---ANTDEI----- 110
           ENFGCGSSRE A  A+   G K VIA SFA IFY N+ N  L+P+    A  DE+     
Sbjct: 78  ENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPVTLSEAQVDELFKLVH 137

Query: 111 -KDGDIVEIDLDKEEIVITNKNKTIKCE 137
            + G   E+DL+ E +   +K+ + K +
Sbjct: 138 SQPGIKFEVDLESEVVKAGDKSYSFKID 165


Lambda     K      H
   0.318    0.139    0.399 

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: 99
Number of extensions: 4
Number of successful extensions: 2
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: 170
Length of database: 201
Length adjustment: 19
Effective length of query: 151
Effective length of database: 182
Effective search space:    27482
Effective search space used:    27482
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: 44 (21.6 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