GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Magnetospirillum magneticum AMB-1

Align Carbamoyl-phosphate synthase small chain; EC 6.3.5.5; Carbamoyl-phosphate synthetase glutamine chain (uncharacterized)
to candidate WP_011385238.1 AMB_RS14405 type 1 glutamine amidotransferase

Query= curated2:Q8KGA2
         (366 letters)



>NCBI__GCF_000009985.1:WP_011385238.1
          Length = 196

 Score = 88.2 bits (217), Expect = 2e-22
 Identities = 57/178 (32%), Positives = 85/178 (47%), Gaps = 12/178 (6%)

Query: 189 NIIRQLNAEGCKVTVV-NAKTTADEVLAMNPDGIFLSNGPGDPFAVTYAIDTIRELAARN 247
           N+   L   G +V V  N   T D+VL + P GI +S GP DP      ++ I   A   
Sbjct: 14  NLWHYLGELGAEVVVKRNDAVTVDQVLGLRPQGIVISPGPCDPDRAGICLELIERAAG-- 71

Query: 248 STLPIFGICLGHQLLSLAFGAKTYKLKFGHHGANHPVKNLLSNTIE------ITSQNHGF 301
            T+P+FG+CLGHQ +  AFG K  +     HG    + +  +   +        ++ H  
Sbjct: 72  -TIPLFGVCLGHQAIGQAFGGKVVRAPKPMHGKVDTITHDDTGVFQGLPSPFRATRYHSL 130

Query: 302 AVEMESLPGELELTHKNLYDMTVEGIRHRELPCFSVQYHPEAAPGPHDSHYLFKEFTE 359
            VE ES P  L ++     D  V G+ H+ELP + VQ+HPE+    H  H + + F +
Sbjct: 131 VVERESFPDCLHVSAWTA-DGLVMGLAHKELPIWGVQFHPESIETEH-GHAMLRNFID 186


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: 203
Number of extensions: 9
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: 196
Length adjustment: 25
Effective length of query: 341
Effective length of database: 171
Effective search space:    58311
Effective search space used:    58311
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 Apr 09 2024. The underlying query database was built on Apr 09 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