GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Synechococcus elongatus PCC 7942

Align ornithine δ-aminotransferase (EC 2.6.1.13) (characterized)
to candidate Synpcc7942_0645 Synpcc7942_0645 glutamate-1-semialdehyde aminotransferase

Query= metacyc::MONOMER-16810
         (468 letters)



>FitnessBrowser__SynE:Synpcc7942_0645
          Length = 453

 Score =  135 bits (340), Expect = 3e-36
 Identities = 90/299 (30%), Positives = 145/299 (48%), Gaps = 27/299 (9%)

Query: 54  PMVFSKAKDVHVWDPEGRKYLDFLSAYSAVNQGHCHEKILNALSQQAQQLTLSSR--AFH 111
           P+VF + KD + WD +G +Y+D++  +     GH H +++ AL    ++ T      A  
Sbjct: 61  PIVFDRVKDAYAWDVDGNRYIDYVGTWGPAICGHAHPEVIEALKVAMEKGTSFGAPCALE 120

Query: 112 NDIFPIFAQHLTSMFGYEMILPMNTGAEGVETALKLARKWGYEKKHIPKNEAIIISCCGC 171
           N +  +    + S+   EM+  +N+G E     L+L R +    K        II   GC
Sbjct: 121 NVLAEMVIDAVPSI---EMVRFVNSGTEACMAVLRLMRAYTGRDK--------IIKFEGC 169

Query: 172 FHGRTTAVISMSCDNEATRGFGPFLPGL--------LKVDFGDADSLKSMFEAHGDKVAG 223
           +HG     +  +    AT G  P  PG+        L   + D +++K++F  +  ++AG
Sbjct: 170 YHGHADMFLVKAGSGVATLGL-PDSPGVPKSTTANTLTAPYNDLEAVKALFAENPGEIAG 228

Query: 224 FLFEPIQGEAGVIVPPKGYLQSVRELCSKYNVLMIADEIQTGIGRTGKLLACEWESVRPD 283
            + EPI G +G IVP  G+L+ +RE+  +++ L++ DE+ TG  R       E   V PD
Sbjct: 229 VILEPIVGNSGFIVPDAGFLEGLREITLEHDALLVFDEVMTGF-RIAYGGVQEKFGVTPD 287

Query: 284 VVILGKALGGGVLPVSAVLADKDIMLCFKPG---EHGSTFGGNPLASAVAIAALEIVEE 339
           +  LGK +GGG LPV A    ++IM    P        T  GNPLA    I  LE++ +
Sbjct: 288 LTTLGKIIGGG-LPVGAYGGKREIMQLVAPAGPMYQAGTLSGNPLAMTAGIKTLELLRQ 345


Lambda     K      H
   0.319    0.136    0.405 

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: 456
Number of extensions: 27
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: 468
Length of database: 453
Length adjustment: 33
Effective length of query: 435
Effective length of database: 420
Effective search space:   182700
Effective search space used:   182700
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: 51 (24.3 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