GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysE in Desulfovibrio vulgaris Miyazaki F

Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate 8501167 DvMF_1901 transferase hexapeptide repeat containing protein (RefSeq)

Query= BRENDA::Q6F4D7
         (295 letters)



>FitnessBrowser__Miya:8501167
          Length = 212

 Score = 58.5 bits (140), Expect = 1e-13
 Identities = 38/118 (32%), Positives = 62/118 (52%), Gaps = 9/118 (7%)

Query: 144 LELGDDVVVHRYVFLDDIGG-IKIGDRTSLSDYVNVYSHTHHVLASPDVTLK-------E 195
           LE+ ++  ++  V +D  GG I++G   ++     + +  H+     DV +        E
Sbjct: 88  LEMAENAALNVNVVVDADGGHIRMGAHVTVGPGTVIRAANHN-FDRTDVPIMFQGHEYGE 146

Query: 196 TIIGSGVRITYHATVLAGVRIGDDAMVGTGAVVTKDIPPHAIALGIPARPVRYKVRHD 253
             I   V I  + T+  GV IG  A+VG GAVVTKD+ P+ +  G+PARP+R +  H+
Sbjct: 147 VTIEDDVWIAANCTITPGVHIGRGAVVGAGAVVTKDVEPYTVVGGVPARPLRKRGVHE 204


Lambda     K      H
   0.321    0.142    0.437 

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: 187
Number of extensions: 12
Number of successful extensions: 1
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: 295
Length of database: 212
Length adjustment: 24
Effective length of query: 271
Effective length of database: 188
Effective search space:    50948
Effective search space used:    50948
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: 46 (22.3 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