GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Marinobacter adhaerens HP15

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate GFF3375 HP15_3317 acetylglutamate kinase

Query= BRENDA::Q87EL2
         (421 letters)



>FitnessBrowser__Marino:GFF3375
          Length = 298

 Score =  121 bits (303), Expect = 3e-32
 Identities = 86/282 (30%), Positives = 139/282 (49%), Gaps = 24/282 (8%)

Query: 10  YLKRFSQLDAKRFAVVKVGGAVLRDD--VDALTSSLSFLQEVGLTPIVLHGAGPQLDEEL 67
           Y++RF+     +  V+K GG  + ++    +    +  ++ VG+ PIV+HG GPQ+ E L
Sbjct: 21  YIQRFTG----KTVVIKYGGNAMENEDLKSSFARDVVLMKLVGINPIVVHGGGPQIGELL 76

Query: 68  TAVGIQKKTVNGFRVTLPETMAIVRKVFHA-TNLQLIEALQRNGARATSITG---GVFEA 123
             + IQ + VNG RVT  ETM +V  V     N +++  +  +G  A  +TG    +  A
Sbjct: 77  ERLNIQSRFVNGMRVTDSETMDVVEMVLGGQVNKEIVSLINSHGGMAVGLTGKDANLIRA 136

Query: 124 HYLDQET------------YGLVGGISAVNIAPIEASLRAASIPVIASLGETPSGQILNI 171
             L+                G VG +++VN+  IE   R+  IPVIA +G  P G   NI
Sbjct: 137 RKLEVVDRSPELERPEIIDIGHVGEVASVNVDVIEMLTRSNLIPVIAPIGVGPDGASYNI 196

Query: 172 NADVAANELVHVLQPYKIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQPWVYGGMKLK 231
           NAD+ A ++   ++  K++ LT   GL   + K++  +  + +   LI+   ++GGM  K
Sbjct: 197 NADLVAGKVAEAMKAEKLMLLTNVSGLKSKEDKVLTGLT-AKQVNDLIEDGTIHGGMLPK 255

Query: 232 IEQIKHLLDRLPLESSVSITRPADLA-KELFTHKGSGTLIRR 272
           I      ++     S +   R A     E+FT +G GTLI R
Sbjct: 256 IRCALSAVENGVRTSHIIDGRVAHACLLEIFTDEGVGTLISR 297


Lambda     K      H
   0.320    0.136    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: 262
Number of extensions: 16
Number of successful extensions: 3
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: 421
Length of database: 298
Length adjustment: 29
Effective length of query: 392
Effective length of database: 269
Effective search space:   105448
Effective search space used:   105448
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