GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Streptacidiphilus oryzae TH49

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_037570915.1 BS73_RS08925 acetylornithine transaminase

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



>NCBI__GCF_000744815.1:WP_037570915.1
          Length = 395

 Score =  273 bits (698), Expect = 6e-78
 Identities = 159/379 (41%), Positives = 218/379 (57%), Gaps = 12/379 (3%)

Query: 5   VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64
           +M  Y    I   RGEG +++  DG+R+ D  AG+AVN LGH +P +V A+T Q + L H
Sbjct: 15  LMNNYGTPRIPLARGEGAHVWDADGKRYTDLVAGIAVNALGHGHPAVVGAVTEQINTLGH 74

Query: 65  TSNLFRVAGQESLAKRLTEATFAD-TVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRII 123
            SNLF       L++RL E       VFF NSGAEA E   K+ R          R  ++
Sbjct: 75  VSNLFIAEPPVRLSERLLELFGRPGRVFFCNSGAEANEGAFKIGRL-------TGRRHMV 127

Query: 124 TFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPI 183
                FHGRT+ A+S   Q     GF PL    + VP+GD+EA+R AVT+ETA   +EP+
Sbjct: 128 ATTGGFHGRTMGALSLTGQPGKQDGFAPLPGDVEFVPYGDVEALRAAVTEETAFFIVEPV 187

Query: 184 QGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAK 243
           QGE G       +L   REI    G LL +DE+Q G+GRTG  FAH+ AGI PDV+ +AK
Sbjct: 188 QGENGAVPAPDGYLEAAREITRAKGALLVVDEVQTGIGRTGHWFAHQAAGIEPDVVTLAK 247

Query: 244 GIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIG 303
           G+GGG P+GA +A   AA  +  G HG+T+GGNP+  A G AVLD + + G LDHV+R+G
Sbjct: 248 GLGGGLPIGATVAFGAAAELLQPGQHGTTFGGNPVCCAAGLAVLDTIAQDGLLDHVKRVG 307

Query: 304 GLLQDRLAGLVAENPAVFKGVRGKGLMLGLA-CGPAVGDVVVALRANGLLSVPAGDNVVR 362
             L+   +G+ +    +   VRG GL+LG+    P    V  A +  G L    G ++VR
Sbjct: 308 ERLR---SGIESIGDPLVARVRGTGLLLGIVLTEPLAPQVQAAAQRAGFLVNATGPDLVR 364

Query: 363 LLPPLNIGEAEVEEAVAIL 381
           L+PPL + E + +  +A+L
Sbjct: 365 LVPPLTLPEVDADAFLAVL 383


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: 474
Number of extensions: 30
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: 395
Length adjustment: 31
Effective length of query: 358
Effective length of database: 364
Effective search space:   130312
Effective search space used:   130312
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