GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Dinoroseobacter shibae DFL-12

Align Carbamoyl-phosphate synthase small chain; EC 6.3.5.5; Carbamoyl-phosphate synthetase glutamine chain (uncharacterized)
to candidate 3608398 Dshi_1798 glutamine amidotransferase of anthranilate synthase (RefSeq)

Query= curated2:Q72PK5
         (363 letters)



>FitnessBrowser__Dino:3608398
          Length = 201

 Score = 64.7 bits (156), Expect = 2e-15
 Identities = 55/179 (30%), Positives = 74/179 (41%), Gaps = 12/179 (6%)

Query: 188 NILRLLDANGFAVTVYPAKTPS-EEIMKEGTDAFFLSNGPGDPAPLDYAIASTQKIMEKR 246
           N++  L   G  V VY       +  M     A  LS GP DP      +A T+   E R
Sbjct: 14  NLVHYLGELGAPVEVYRNDALDVQAAMALNPQAILLSPGPCDPDQAGICLALTEAAAETR 73

Query: 247 YPLFGICLGHQIIGLSLGKKTE--------KMKFGHRGGNQPVKNLETGQVEITSQNHGF 298
            PL G+CLGHQ IG + G K +        K+   H GG      L +    + ++ H  
Sbjct: 74  TPLIGVCLGHQTIGQAFGGKVQRHSEIVHGKLGAMHHGGTGLFAGLPSPL--MGTRYHSL 131

Query: 299 AVIDDQKQDEPISFLNLNDHTVEGILKSGYPLLTVQYHPESAPGPNDSRYLFQKFYDLV 357
            V  D   D       L D T+ G+     P+  VQ+HPES    +  + L Q F D V
Sbjct: 132 VVDRDTLPDCLEVTAWLEDGTIMGLQHRELPIHGVQFHPESIKSEHGHKML-QNFLDTV 189


Lambda     K      H
   0.316    0.136    0.393 

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: 181
Number of extensions: 10
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: 363
Length of database: 201
Length adjustment: 25
Effective length of query: 338
Effective length of database: 176
Effective search space:    59488
Effective search space used:    59488
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 (21.6 bits)
S2: 47 (22.7 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