GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Amycolatopsis halophila YIM 93223

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_034272173.1 AMYHA_RS15990 acetylornithine transaminase

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



>NCBI__GCF_000504245.1:WP_034272173.1
          Length = 393

 Score =  267 bits (682), Expect = 4e-76
 Identities = 154/379 (40%), Positives = 216/379 (56%), Gaps = 12/379 (3%)

Query: 5   VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64
           +M  Y    +   RG+G  ++  DG  +LD   G+AVN LGHA+P +VEA++ Q   L H
Sbjct: 11  MMDNYGTPALELVRGDGATVFDADGNAYLDLVGGIAVNALGHAHPAVVEAVSEQVATLGH 70

Query: 65  TSNLFRVAGQESLAKRLTE-ATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRII 123
           TSNL+      SLA+ L + A  +  V F NSGAEA E   K+ R          +++++
Sbjct: 71  TSNLYINPVALSLAETLLDIAGLSGKVLFCNSGAEAVEAAIKITRL-------TGKSKLV 123

Query: 124 TFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPI 183
             +  FHGRT+ A+S   Q    + F PLL G   VPFGD  A+ +AV  +TA + +EP+
Sbjct: 124 ACDGGFHGRTMGALSVTGQPSKREPFEPLLPGVTHVPFGDTAALESAVDGDTAAVFVEPV 183

Query: 184 QGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAK 243
            GEGG+      FLR  REI    G LL LDE+Q G+GR G  FA + AG+TPDV+ +AK
Sbjct: 184 LGEGGVVPAPDGFLRAAREIATAAGALLVLDEVQTGIGRLGSWFAFQQAGVTPDVITLAK 243

Query: 244 GIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIG 303
           G+GGG PLGA +   +    +  G HG+T+GGNP+A A G+AV+  + E G LDHV+ +G
Sbjct: 244 GLGGGLPLGAVIGIGQTGELLKPGQHGTTFGGNPIACAAGHAVIRTIREQGLLDHVETLG 303

Query: 304 GLLQDRLAGLVAENPAVFKGVRGKGLMLGLA-CGPAVGDVVVALRANGLLSVPAGDNVVR 362
              +D  AG+   +  +   VRG GL+ G+    P    V  A +  G L  P   +V+R
Sbjct: 304 ---KDLAAGVRKLDHPLVSEVRGAGLLQGIGLTKPVAPTVATAAQRAGYLINPVQPDVIR 360

Query: 363 LLPPLNIGEAEVEEAVAIL 381
           L PPL I E +V + +A L
Sbjct: 361 LAPPLIITERQVADFLAAL 379


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: 493
Number of extensions: 39
Number of successful extensions: 5
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: 393
Length adjustment: 31
Effective length of query: 358
Effective length of database: 362
Effective search space:   129596
Effective search space used:   129596
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 26 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