GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysE in Enterococcus termitis LMG 8895

Align Serine O-acetyltransferase; SAT; Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_069665168.1 BCR25_RS18890 homoserine O-succinyltransferase

Query= SwissProt::A0A1D3PCK2
         (262 letters)



>NCBI__GCF_001730305.1:WP_069665168.1
          Length = 309

 Score =  124 bits (311), Expect = 2e-33
 Identities = 75/256 (29%), Positives = 125/256 (48%), Gaps = 11/256 (4%)

Query: 5   VKIGILNLMHDKLDTQSHFIKVLPNADLT----FFYPRMHYQNRPIPPEVNMTSEPLDIN 60
           ++I ILNLM  K +T+   +++L N  L     F +   H         +          
Sbjct: 36  LQILILNLMPKKDETEVQLLRLLSNTPLQINVDFLHMSSHEAKNTSKDHLKRFYHQFSDV 95

Query: 61  RVSEFDGFIITGAPIDQIDFSKITYIEEIRYLLQALDNHKIQQLYFCWGAMAALNYFYGI 120
           +   +DG I+TGAP++Q+ F ++ Y  E+  + Q    H     + CWGA A L Y + I
Sbjct: 96  KEKYYDGLIVTGAPVEQLPFEEVDYWNELTDIFQWSKTHVFSTFHICWGAQAGLYYHHHI 155

Query: 121 KKKILAEKIFGVFPH-LITEPHPLLSGLSQGFMAPHARYAEMDKKQIMQDERLAINAVDD 179
           +K  L +K+ G++ H ++T    +L G    F+APH+RY  +++  I   E LAI A   
Sbjct: 156 QKHPLDKKLSGIYLHDVLTPTWSILKGFDDVFLAPHSRYTTVNRAAIEGVEELAILAESA 215

Query: 180 NSHLFMVSAKDNPERNFIFSHIEYGKDSLRDEYNRE----INAHPERHYKKPINYSMSNP 235
            + +F+V  K+N    +   H+EY +++L+ E+ R+    I      HY  P + S   P
Sbjct: 216 EAGIFLVGNKNN-RAFYAMGHLEYDRETLQQEFYRDQAKGIRPKLPEHY-FPNDDSQKYP 273

Query: 236 SFQWQDTQKIFFNNWL 251
             +W     + F+NWL
Sbjct: 274 QLRWHMAASLLFSNWL 289


Lambda     K      H
   0.322    0.138    0.420 

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: 211
Number of extensions: 11
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: 262
Length of database: 309
Length adjustment: 26
Effective length of query: 236
Effective length of database: 283
Effective search space:    66788
Effective search space used:    66788
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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