GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argF' in Escherichia coli BW25113

Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate 18279 b4254 ornithine carbamoyltransferase 1 (NCBI)

Query= BRENDA::Q8P8J2
         (339 letters)



>FitnessBrowser__Keio:18279
          Length = 334

 Score =  130 bits (328), Expect = 4e-35
 Identities = 112/362 (30%), Positives = 164/362 (45%), Gaps = 63/362 (17%)

Query: 4   KHFLNTQDWSRAELDALLTQAALFKRNKLG----SELKGKSIALVFFNPSMRTRTSFELG 59
           KHFL   D++ AEL++LL  AA  K +K      ++L GK+IAL+F   S RTR SFE+ 
Sbjct: 7   KHFLKLLDFTPAELNSLLQLAAKLKADKKSGKEEAKLTGKNIALIFEKDSTRTRCSFEVA 66

Query: 60  AFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVD 119
           A+  G     L P          +G       +E I + ARVLGR  D I  R + +   
Sbjct: 67  AYDQGARVTYLGPSGS------QIG------HKESIKDTARVLGRMYDGIQYRGYGQ--- 111

Query: 120 WSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTWT 178
                  +++++ A+Y+ VPV N +    HP Q LA  L +QEH     L GK +     
Sbjct: 112 -------EIVETLAEYASVPVWNGLTNEFHPTQLLADLLTMQEH-----LPGKAFNEMTL 159

Query: 179 YHPKPLNTAVANSALTIATRMGMDVTLLCPT---PDYILDERYMDWAAQNVAESGGSLQV 235
            +       + NS L  A   G+D+ L+ P    P+  L       A QN    GG++ +
Sbjct: 160 VYAGDARNNMGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQN----GGNITL 215

Query: 236 SHDIDSAYAGADVVYAKSWGAL-PFFGNWEPEKPIRDQYQHFIVDERKMALTNNG--VFS 292
           + D+     GAD +Y   W ++      W     +  +YQ   V+ + M LT N    F 
Sbjct: 216 TEDVAKGVEGADFIYTDVWVSMGEAKEKWAERIALLREYQ---VNSKMMQLTGNPEVKFL 272

Query: 293 HCLP------------------LRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334
           HCLP                  L   ++ TD V +S   I  D+AENR+H  KA+M A +
Sbjct: 273 HCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATL 332

Query: 335 GQ 336
            +
Sbjct: 333 SK 334


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: 226
Number of extensions: 15
Number of successful extensions: 6
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: 334
Length adjustment: 28
Effective length of query: 311
Effective length of database: 306
Effective search space:    95166
Effective search space used:    95166
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: 49 (23.5 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