GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Salinicoccus carnicancri Crm

Align Carbamoyl-phosphate synthase small chain; EC 6.3.5.5; Carbamoyl-phosphate synthetase glutamine chain (uncharacterized)
to candidate WP_017549241.1 C792_RS0109535 aminodeoxychorismate/anthranilate synthase component II

Query= curated2:Q8KGA2
         (366 letters)



>NCBI__GCF_000330705.1:WP_017549241.1
          Length = 192

 Score = 70.5 bits (171), Expect = 3e-17
 Identities = 59/175 (33%), Positives = 84/175 (48%), Gaps = 19/175 (10%)

Query: 178 HVVAFDYGIKTNIIRQLNAEGCKVTVV-NAKTTADEVLAMNPDGIFLSNGPGDPFAVTYA 236
           H  +F Y    NI++ L   G  +TV  N     +E+ A+ PD I LS GP  P      
Sbjct: 7   HYDSFTY----NIVQFLGECGEDITVRRNDAVQLNEIEALQPDLILLSPGPRTPEQTGMT 62

Query: 237 IDTIRELAARNSTLPIFGICLGHQLLSLAFG---AKTYKLKFG-----HHGANHPVKNLL 288
           ++ I +       LPIFG+CLGHQ ++ AFG    KT +L  G     HH      + + 
Sbjct: 63  LEVIDKF---KGILPIFGVCLGHQSIAHAFGGNIVKTGRLMHGKTSQIHHDGIGIFRGIP 119

Query: 289 SNTIEITSQNHGFAVEMESLPGELELTHKNLYDMTVEGIRHRELPCFSVQYHPEA 343
             T E+ +  H   V+  SLP   E++ +N     V  IRHR+     VQ+HPE+
Sbjct: 120 QGT-EVMNY-HSLVVDRASLPDCFEVSAEN-EKGEVMAIRHRDFSIEGVQFHPES 171


Lambda     K      H
   0.317    0.134    0.387 

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: 195
Number of extensions: 10
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: 366
Length of database: 192
Length adjustment: 25
Effective length of query: 341
Effective length of database: 167
Effective search space:    56947
Effective search space used:    56947
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 (21.7 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