GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argE'B in Pedobacter sp. GW460-11-11-14-LB5

Align Acetylornithine deacetylase (characterized, see rationale)
to candidate CA265_RS00205 CA265_RS00205 acetylornithine deacetylase

Query= uniprot:A0A1X9Z8E1_9SPHI
         (355 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS00205 CA265_RS00205
           acetylornithine deacetylase
          Length = 366

 Score =  410 bits (1053), Expect = e-119
 Identities = 199/347 (57%), Positives = 259/347 (74%)

Query: 3   LENIQKESLDLLRQLIRIQSFSKEEDRTANLIAQFLEERGIKTQRKMNNVWAYNKHFDAT 62
           L ++ +ESL+LL  LI I S S +E  TA+ I  FL  +GI T RK NN+W YNK+ DA+
Sbjct: 15  LNHLYQESLELLSSLISIPSISGDEMLTADQIETFLNLQGINTFRKHNNIWCYNKYMDAS 74

Query: 63  KPTLLLNSHHDTVKPNSGYTRDPYDAAIEGDKLFGLGSNDAGGCLVSLIGTFLYYYEQEG 122
           KPT+LLNSHHDTV+PN  YTRDP+   IE +K++GLGSNDAGG LV+L  TFLY++E++ 
Sbjct: 75  KPTILLNSHHDTVRPNEQYTRDPFSPIIEEEKIYGLGSNDAGGPLVALTATFLYFFERKD 134

Query: 123 LKYNICLAATAEEEISGNNGLELVLPDLGELEFGIVGEPTEMNLAIAERGLLVLDCVSHG 182
           L +N+CLAATAEEE SG  G+  +LPDL E+ F IVGEPT M++AIAE+G +V+DCVS G
Sbjct: 135 LSFNLCLAATAEEETSGELGIRSILPDLKEISFAIVGEPTGMHMAIAEKGSMVIDCVSKG 194

Query: 183 KAGHAAREEGENAIYKALKDIEWFRNYQFPKVSEVFGPLKMTVTIINAGSQHNVVPANCT 242
           ++GHAAREEG+NAIY ALKDI+WF++Y FP + +   P+KMTVT I AG QHN+VPA C+
Sbjct: 195 RSGHAAREEGDNAIYHALKDIDWFKSYLFPIMDDQPQPVKMTVTEIRAGIQHNIVPAECS 254

Query: 243 FTVDVRVTDAYTNEEVLEIIRANVDCDVTPRSIRLKPSSIDKNHPVVQAGVALGKTTYGS 302
           FTVD+R    Y   E++  I  +  C  T R   LKPS ID  HPVV +G++LG+ TY S
Sbjct: 255 FTVDIRFDHNYNEREIVNTIINHTSCHFTVRPNVLKPSFIDMLHPVVVSGLSLGRKTYLS 314

Query: 303 PTTSDQALLDIPSVKCGPGFSGRSHMADEFLYVREVAEGVEGYVNML 349
           PT+SDQ  LD+PSVK GPG S RSH ADEF+ + E+ EG++ Y+++L
Sbjct: 315 PTSSDQGWLDMPSVKMGPGNSARSHTADEFIGIEEIEEGIDIYISLL 361


Lambda     K      H
   0.317    0.135    0.394 

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: 401
Number of extensions: 9
Number of successful extensions: 1
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: 355
Length of database: 366
Length adjustment: 29
Effective length of query: 326
Effective length of database: 337
Effective search space:   109862
Effective search space used:   109862
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 (21.6 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 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, 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