GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS00205
          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 (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