GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argI in Pedobacter sp. GW460-11-11-14-LB5

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate CA265_RS18520 CA265_RS18520 acetylornithine carbamoyltransferase

Query= curated2:Q8TKT5
         (302 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS18520 CA265_RS18520
           acetylornithine carbamoyltransferase
          Length = 324

 Score =  109 bits (272), Expect = 1e-28
 Identities = 98/321 (30%), Positives = 142/321 (44%), Gaps = 48/321 (14%)

Query: 16  IYELLESAADLKAKRKAGESTEYLKNKSLGMIFEKSSTRTRVSFEVAMTDFGGHALYLN- 74
           I + +  A  LKA   A +     KNK+LG++F   S RTR+S + A  + G + + +N 
Sbjct: 13  IKQFVNDALALKANPYAHQDLG--KNKTLGLVFMNPSLRTRLSTQKAALNLGMNVMVMNL 70

Query: 75  --------SRDIQVGRGETIE---DTARTLSGYLHGLMARVM----------SHDTVEKL 113
                   ++D  V  G T+E   + A  +  Y   L  R            S D   K 
Sbjct: 71  DKEGWALETQDGVVMNGSTVEHIREAAAVMGQYCDILGLRSFPKLNNREEDYSEDFFNKF 130

Query: 114 AKYSTMPVINALSDREHPCQILGDFMTIME-FKKKFEGLK----FAWVGD--------GN 160
            KY  +PV++  S   HP Q   D +TI E + KK +G K     AW            N
Sbjct: 131 VKYCAVPVVSLESATRHPLQSFADIITIHETWTKKPDGRKPKVVLAWAPHVKALPQAVPN 190

Query: 161 NVCNSALLGSAIMGMEFAVACPKGYEPKAEFLEQAKALGGKFTITDDPKVAAKDADIIYT 220
           +         A   ++F +A P+GYE   +F   A        I  + + A   AD +Y 
Sbjct: 191 SFAEWMCKAQAEGMIDFTIAQPEGYELSEDFTPDAN-------IQYNLEEALAGADYVYV 243

Query: 221 DVWVSMGDEAEQEKRLREFASFQVNTELLGVAKPDVIVMHCLPARRGLEITDEVMDGPNS 280
             W S     E  K L     + +N E L     D  VMHCLP RR LE++ E++DGPNS
Sbjct: 244 KNWSSY---KEYGKVLTYPDGWMMNNEKLKFTN-DAKVMHCLPVRRDLELSSEILDGPNS 299

Query: 281 VIFEEAENRLHAQKALILKLM 301
           ++  EA NRL A +A+I  ++
Sbjct: 300 LVIHEAGNRLWAAQAVIKAML 320


Lambda     K      H
   0.318    0.134    0.378 

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: 204
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: 302
Length of database: 324
Length adjustment: 27
Effective length of query: 275
Effective length of database: 297
Effective search space:    81675
Effective search space used:    81675
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: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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