GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Pseudomonas simiae WCS417

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate GFF1577 PS417_08025 acetylornithine aminotransferase

Query= reanno::azobra:AZOBR_RS19025
         (389 letters)



>FitnessBrowser__WCS417:GFF1577
          Length = 389

 Score =  277 bits (709), Expect = 3e-79
 Identities = 165/383 (43%), Positives = 221/383 (57%), Gaps = 6/383 (1%)

Query: 5   VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64
           +M TY    + F RG G  L+   GR +LD  AGVAV  +GH++P LV A++ QA  L H
Sbjct: 6   LMTTYQPLALSFTRGLGTRLWDQQGREYLDAVAGVAVTNVGHSHPRLVAAISEQAGLLLH 65

Query: 65  TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124
           TSNL+ +  Q+ LA+RLT+ +  D  FF NSGAEA E   KL R + ++KG +A   ++ 
Sbjct: 66  TSNLYSIDWQQRLAQRLTQLSGLDRAFFNNSGAEANETALKLARLHGWKKGIEAPL-VVV 124

Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDL---EAVRNAVTDETAGICLE 181
            E AFHGRTL  ++A+    +  GF  L   F  V FGDL   EA+  A       + LE
Sbjct: 125 MENAFHGRTLGTLAASDGPSVRLGFQQLPGDFLKVRFGDLAALEAITKAFGPRITAVLLE 184

Query: 182 PIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAV 241
           PIQGE G+      +L+ LR+ C   G L+ LDEIQ G+GRTG  FA +  GI PDVM +
Sbjct: 185 PIQGESGVLPAPSGYLQALRDHCTRQGWLMMLDEIQTGIGRTGTWFAFQHEGIVPDVMTL 244

Query: 242 AKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQR 301
           AKG+G G P+GACLA    A   T G+HGST+GGNPLA  VG  VLD + E G L +  +
Sbjct: 245 AKGLGNGVPIGACLARAAVAQLFTPGSHGSTFGGNPLACRVGCTVLDIIEEQGLLQNAAQ 304

Query: 302 IGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVV-ALRANGLLSVPAGDNV 360
            G  L  RL   + E+  V   +RG+GLM+G+       D+   A + +GLL       +
Sbjct: 305 QGERLLARLRVELNEHAQVV-AIRGQGLMIGIELASPCRDLAQRAAQEHGLLINVTRGKI 363

Query: 361 VRLLPPLNIGEAEVEEAVAILAK 383
           +RLLPPL +   EVE  V  + +
Sbjct: 364 IRLLPPLTLDTQEVEMIVRAITR 386


Lambda     K      H
   0.321    0.139    0.414 

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: 431
Number of extensions: 21
Number of successful extensions: 4
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: 389
Length of database: 389
Length adjustment: 30
Effective length of query: 359
Effective length of database: 359
Effective search space:   128881
Effective search space used:   128881
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: 50 (23.9 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