GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Allochromatium vinosum DSM 180

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_043795594.1 ALVIN_RS09555 aspartate aminotransferase family protein

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



>NCBI__GCF_000025485.1:WP_043795594.1
          Length = 392

 Score =  326 bits (836), Expect = 6e-94
 Identities = 180/379 (47%), Positives = 241/379 (63%), Gaps = 4/379 (1%)

Query: 5   VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64
           +M TY R  + F+RGEG +L+ T+G+R+LD  +G+AV  LGHA+P + +AL  QA +L H
Sbjct: 5   LMATYNRLPVTFDRGEGVWLWDTNGKRYLDALSGIAVCGLGHAHPAVRDALCEQAGRLIH 64

Query: 65  TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124
           TSN++ VA QE L   LTE    D VFF NSGAEA E   KL R + + +G +    I+ 
Sbjct: 65  TSNIYGVAEQERLGALLTEQAGMDRVFFANSGAEANEAAIKLARLHAHRRGIE-NPAILV 123

Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDET--AGICLEP 182
            E +FHGRTLA +SA    K+  GF PL+ GF  VP+ DL+A+  A T+      I +EP
Sbjct: 124 AEHSFHGRTLATLSATGNRKVQAGFEPLVQGFVRVPYDDLDAIETAATNRPNIVAILIEP 183

Query: 183 IQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVA 242
           IQGEGGIR  S ++L  LREICD  G LL LDEIQ GMGRTG+LFA + AGI PDV+ +A
Sbjct: 184 IQGEGGIRLPSDDYLVRLREICDRSGWLLMLDEIQTGMGRTGRLFAFQHAGIQPDVVTLA 243

Query: 243 KGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRI 302
           KG+G G P+GACLA   AA   + G+HGST+GGNPLA  VG AVL+ +++    ++    
Sbjct: 244 KGLGNGMPIGACLARGAAAEVFSPGSHGSTFGGNPLACRVGRAVLETLIDENLTENAAAQ 303

Query: 303 GGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVR 362
           G  L D L   + E   + + +RG+GLM+G+      G++V      GLL     + V+R
Sbjct: 304 GAYLLDSLRAALGETHGLVE-IRGRGLMVGIELDRPCGELVGRALDAGLLINVTAERVIR 362

Query: 363 LLPPLNIGEAEVEEAVAIL 381
           LLPPL I  A+++E VA L
Sbjct: 363 LLPPLIIDRAQIDELVATL 381


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: 480
Number of extensions: 26
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: 392
Length adjustment: 31
Effective length of query: 358
Effective length of database: 361
Effective search space:   129238
Effective search space used:   129238
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 Jul 25 2024. The underlying query database was built on Jul 25 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