GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argI in Cereibacter sphaeroides ATCC 17029

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_002721320.1 RSPH17029_RS13430 aspartate carbamoyltransferase catalytic subunit

Query= curated2:Q8DVC9
         (326 letters)



>NCBI__GCF_000015985.1:WP_002721320.1
          Length = 320

 Score = 72.8 bits (177), Expect = 1e-17
 Identities = 58/178 (32%), Positives = 88/178 (49%), Gaps = 4/178 (2%)

Query: 17  EIEDFIDLAMQFKKLKKERIPHR-YFDGLNIALIFEKTSTRTRSAFTVAGQDLGMNVSYL 75
           EI   +DLA  +  L +  +       G+    +F + STRT+S+F +AG+ LG +V  +
Sbjct: 18  EIRSVLDLADSYVDLNRRTMKQSDALAGMTQINMFFENSTRTQSSFELAGKRLGADVMNM 77

Query: 76  GKDDIQLGKKESLVDTAKVLGTMF-DGIEYRGFKQESVELLAEFSGVPVWN-GLTDTWHP 133
                 + K E+L+DTA  L  M  D +  R     +V LLA      V N G     HP
Sbjct: 78  AVAQSSVKKGETLLDTAMTLNAMHPDLLVVRHPASGAVNLLASKVNCAVLNAGDGRHEHP 137

Query: 134 TQMIADFMTVKEHFGKFEDLTLAYLGD-GRNNVANSLLVTSAILGINVKIIAPKELQP 190
           TQ + D +T++   G+ + LT+A  GD   + VA S L+    +   V++IAP  L P
Sbjct: 138 TQALLDALTIRRAKGRIQRLTVAICGDIAHSRVARSNLILLGKMENRVRLIAPPTLMP 195


Lambda     K      H
   0.319    0.136    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: 200
Number of extensions: 15
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: 326
Length of database: 320
Length adjustment: 28
Effective length of query: 298
Effective length of database: 292
Effective search space:    87016
Effective search space used:    87016
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: 48 (23.1 bits)

This GapMind analysis is from Apr 16 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