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_037575525.1 BS73_RS23310 ornithine--oxo-acid transaminase

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



>NCBI__GCF_000744815.1:WP_037575525.1
          Length = 391

 Score =  231 bits (588), Expect = 3e-65
 Identities = 143/379 (37%), Positives = 201/379 (53%), Gaps = 7/379 (1%)

Query: 9   YARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNL 68
           Y    +V E  EG ++  T GRR+LD  AG +    GH +P L+ A   Q  ++  TS  
Sbjct: 9   YHPLPVVIESAEGAWVTDTAGRRYLDLLAGYSALNFGHRHPRLIAAAERQLGRVTLTSRA 68

Query: 69  FRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYE-KGDKART-RIITFE 126
           F+        ++L +    + V   N+GAEA E   K  R++ Y  KG  A T +I+   
Sbjct: 69  FQHDLFAPFCEQLADLCGMEAVLPMNTGAEAVETAIKTARRWAYRVKGVPADTAKIVAAR 128

Query: 127 QAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQGE 186
             FHGRT   V  +  E+   GFGP   GF+LVP+GD+EA+  AV D TA + LEPIQGE
Sbjct: 129 GNFHGRTTTIVGFSDDEEARDGFGPFTPGFELVPYGDVEALSAAVDDRTAAVLLEPIQGE 188

Query: 187 GGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGIG 246
            G+      +L   R I +E G+LL  DEIQ G+GRTG+ FA E  G+ PD   + K +G
Sbjct: 189 AGVIVPPPGYLAEARRITEERGVLLIADEIQSGLGRTGRTFACEHEGVVPDAYILGKALG 248

Query: 247 GG-FPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGL 305
           GG  P+ A +++       T G+HGST+GGNPLA AV   V+  +    +      +G  
Sbjct: 249 GGVLPISAVVSSRAVMDVFTPGSHGSTFGGNPLACAVALEVIALLRTGAYQRRAAELGAR 308

Query: 306 LQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVG---DVVVALRANGLLSVPAGDNVVR 362
           L   LA L A+       VRG+GL  G+   PAVG   ++   L A G+L+     + +R
Sbjct: 309 LHRELAEL-ADGDWPVTAVRGRGLWAGVDVSPAVGTGREICERLMARGVLAKDTHGSTIR 367

Query: 363 LLPPLNIGEAEVEEAVAIL 381
           + PPL I E ++  A+A L
Sbjct: 368 VAPPLVISEEDLSWALAQL 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: 443
Number of extensions: 24
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: 391
Length adjustment: 31
Effective length of query: 358
Effective length of database: 360
Effective search space:   128880
Effective search space used:   128880
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