GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argF' in Dyella japonica UNC79MFTsu3.2

Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate N515DRAFT_3763 N515DRAFT_3763 N-acetylornithine carbamoyltransferase

Query= BRENDA::Q8P8J2
         (339 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3763
          Length = 335

 Score =  563 bits (1452), Expect = e-165
 Identities = 270/336 (80%), Positives = 303/336 (90%), Gaps = 2/336 (0%)

Query: 1   MSLKHFLNTQDWSRAELDALLTQAALFKRNKLGSELKGKSIALVFFNPSMRTRTSFELGA 60
           M+L+HFL TQD+SRAE+DALL QAA FKR+  G +L GKS+AL+FFNPSMRTRTSFELGA
Sbjct: 1   MTLRHFLTTQDYSRAEIDALLEQAAAFKRSPRGQQLAGKSVALLFFNPSMRTRTSFELGA 60

Query: 61  FQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVDW 120
           F LGGHA+VL PGKDAWPIEF++GTVMDGDTEEHIAEVARVL RYVDLI VRAFPKF DW
Sbjct: 61  FHLGGHAIVLAPGKDAWPIEFDVGTVMDGDTEEHIAEVARVLSRYVDLIAVRAFPKFQDW 120

Query: 121 SKDREDQVLKSFAKYSPVPVINMETITHPCQELAHALALQEHFGTPDLRGKKYVLTWTYH 180
           + DRED+V+K+FA+Y+ VPVINMETITHPCQELAHALA+QEH G+  L+ KKYVLTWTYH
Sbjct: 121 TVDREDRVIKAFAQYASVPVINMETITHPCQELAHALAMQEHLGS--LQNKKYVLTWTYH 178

Query: 181 PKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHDID 240
           PKPLNTAVANSAL IAT+MGMDVTLLCPTPDY+LD+RYM     N   +GGSL++SHDID
Sbjct: 179 PKPLNTAVANSALLIATKMGMDVTLLCPTPDYVLDDRYMQAGYANAQANGGSLRISHDID 238

Query: 241 SAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTNNGVFSHCLPLRRN 300
            AY+GADVVYAKSWGALPFFG WE EKPIRD ++HFIVDERKMALTNNG+FSHCLPLRRN
Sbjct: 239 EAYSGADVVYAKSWGALPFFGRWEQEKPIRDAHKHFIVDERKMALTNNGLFSHCLPLRRN 298

Query: 301 VKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVGQ 336
           VKATDAVMD+P CIAIDEAENRLHVQKA+MA L+GQ
Sbjct: 299 VKATDAVMDAPYCIAIDEAENRLHVQKAVMATLLGQ 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: 467
Number of extensions: 17
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: 335
Length adjustment: 28
Effective length of query: 311
Effective length of database: 307
Effective search space:    95477
Effective search space used:    95477
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 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 (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