GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Desulfovibrio vulgaris Miyazaki F

Align L-amino acid N-acyltransferase MnaT; L-methionine N-acyltransferase; L-methionine sulfoximine/L-methionine sulfone N-acetyltransferase; L-phenylglycine N-acetyltransferase; EC 2.3.1.- (characterized)
to candidate 8499697 DvMF_0463 GCN5-related N-acetyltransferase (RefSeq)

Query= SwissProt::P76112
         (172 letters)



>FitnessBrowser__Miya:8499697
          Length = 178

 Score =  197 bits (500), Expect = 1e-55
 Identities = 99/175 (56%), Positives = 117/175 (66%), Gaps = 5/175 (2%)

Query: 1   MSIRFARKADCAAIAEIYNHAVLYTAAIWNDQTVDADNRIAWFEARTLAGYPVLVSEENG 60
           M IR A   D   I  IYN AV  T AIWN+   DA  R AW   R  AG+PVLV+ E G
Sbjct: 1   MLIRDAESGDIEGIVAIYNDAVCNTTAIWNESVTDAAGRAAWLADRRAAGHPVLVAVEAG 60

Query: 61  -----VVTGYASFGDWRSFDGFRHTVEHSVYVHPDHQGKGLGRKLLSRLIDEARDCGKHV 115
                VV GYA+FGDWR++DG+RHTVEHSVYVH D +G+GLG  LL  LI  ARD GKHV
Sbjct: 61  RNGGPVVLGYATFGDWRAWDGYRHTVEHSVYVHKDTRGRGLGAALLHALIGRARDMGKHV 120

Query: 116 MVAGIESQNQASLHLHQSLGFVVTAQMPQVGTKFGRWLDLTFMQLQLDERTEPDA 170
           MVAG+E+ N+AS+ LH+ +GF     + +VG KFGRWLDL F+QL LD R  P A
Sbjct: 121 MVAGVEAGNEASMALHRKMGFTEVGMLREVGCKFGRWLDLAFLQLTLDARETPPA 175


Lambda     K      H
   0.322    0.136    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: 128
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: 172
Length of database: 178
Length adjustment: 19
Effective length of query: 153
Effective length of database: 159
Effective search space:    24327
Effective search space used:    24327
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: 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