GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argF' in Thermus aquaticus YT-1

Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate WP_053767952.1 BVI061214_RS08055 ornithine carbamoyltransferase

Query= BRENDA::Q8P8J2
         (339 letters)



>NCBI__GCF_001280255.1:WP_053767952.1
          Length = 301

 Score =  118 bits (296), Expect = 2e-31
 Identities = 101/334 (30%), Positives = 157/334 (47%), Gaps = 46/334 (13%)

Query: 4   KHFLNTQDWSRAELDALLTQAALFKRNKL-GSELKGKSIALVFFNPSMRTRTSFELGAFQ 62
           K  L+   +++  L  LL  A   KR +  G +LKGKS+AL+F  PS+RTRT+ E+    
Sbjct: 10  KDLLDFSGYTKEALKRLLDLAEALKRERYRGEDLKGKSLALLFEKPSLRTRTTLEVAMVH 69

Query: 63  LGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVDWSK 122
           LGGHA+ L         +  +G        E + ++A+ L R+V+ I  R +        
Sbjct: 70  LGGHALYLDQK------QVGIG------EREPVRDIAKNLERFVEGIAARVY-------- 109

Query: 123 DREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTWTYHP 181
               + ++  A+++ +PVIN +    HP Q LA  L L+E FG   L G +  + W    
Sbjct: 110 --RHRTVEELARHARIPVINALSDRAHPLQALADLLTLKEAFG--GLEGLE--VAWVGD- 162

Query: 182 KPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHDIDS 241
                 V  S L +A  +G+ V +  P        R  +  A  +A +G  L  +HD   
Sbjct: 163 ---GNNVLASLLEVAPLVGLKVRVATP--------RGYEPEAALLARAGAFL--THDPKE 209

Query: 242 AYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTN-NGVFSHCLPLRRN 300
           A  GA  +Y   W ++      E EK +RD +Q F  +   + L +  G+F HCLP    
Sbjct: 210 AVLGAHALYTDVWTSMG--QEAEREKRLRD-FQGFQANGPLLDLLHPEGIFLHCLPAHYG 266

Query: 301 VKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334
            + T+  +  P     D+AENRLH  KA++  L+
Sbjct: 267 EETTEEAVFGPRSRVFDQAENRLHTAKAVLLTLL 300


Lambda     K      H
   0.320    0.134    0.412 

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: 230
Number of extensions: 13
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: 339
Length of database: 301
Length adjustment: 28
Effective length of query: 311
Effective length of database: 273
Effective search space:    84903
Effective search space used:    84903
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 Jul 25 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