GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Phaeobacter inhibens BS107

Align alanine-glyoxylate transaminase (EC 2.6.1.44); serine-glyoxylate transaminase (EC 2.6.1.45) (characterized)
to candidate GFF2363 PGA1_c23940 putative serine-glyoxylate aminotransferase

Query= BRENDA::Q56YA5
         (401 letters)



>FitnessBrowser__Phaeo:GFF2363
          Length = 421

 Score =  235 bits (600), Expect = 2e-66
 Identities = 143/400 (35%), Positives = 219/400 (54%), Gaps = 20/400 (5%)

Query: 2   DYMYGPGRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGT 61
           D     GR +L +PGP  IP+ V++AM+R + +  +  +  +T TL+ D++++ +T    
Sbjct: 4   DVSLAAGRGYLAIPGPSVIPDAVLQAMHRPSPNIYAGELVEMTATLIPDLRRVARTEHNV 63

Query: 62  PFLFPTTGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGA 121
             ++ + G GAWE+AL NTL PGD ++    G+F++ W +  + L   V++++   G   
Sbjct: 64  A-IYISNGHGAWEAALQNTLQPGDTVLVASSGRFAIGWSEMAEALGIKVELLDFGTGAPW 122

Query: 122 NLQVLASKLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSIC 181
           ++  +AS L+ D  H IKA+  VH +T++ + ND++A+R  LD   HPALL+ D ++S+ 
Sbjct: 123 DMDRIASHLAADTAHRIKAVLAVHVDTSSSIRNDVAAMRAALDACDHPALLMADCIASLG 182

Query: 182 ALDFRMDEWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFY 241
              F MD WGVDV +   QK L +P G+G V  SPKA EA      +  ++DW       
Sbjct: 183 CDRFEMDAWGVDVMVAACQKGLMVPAGMGFVFFSPKAAEARARLPRVSRYWDWEPRANPE 242

Query: 242 KLGTYWPYTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWG----LKNC 297
           +   Y+  T     LYGLRAALDLI  EG+E + ARH RL +A   A + WG    L+  
Sbjct: 243 EFYQYFGGTAPTHHLYGLRAALDLIHGEGMEAVWARHHRLAQAIWAACDRWGDGGPLRMN 302

Query: 298 TQKEEWISNTVTAVMVPPHIDGSEIVR-RAW--QRYNLSLGLGLNKVAGK------VFRI 348
            Q     SN VT++    H+ G E  R R W  Q   L+LG+GL              R+
Sbjct: 303 VQDVALRSNAVTSL----HLGGDEATRLRTWVEQTLGLTLGIGLGMAPPNSPEWHGFLRL 358

Query: 349 GHLGNVNELQLLGCLAGVEMILKDVGYPVVMGSGVAAAST 388
           GH+G+V+   ++G L GV+  LK +  P   GSG   A++
Sbjct: 359 GHMGHVSGQMIMGLLGGVDAGLKALEIP--HGSGALEAAS 396


Lambda     K      H
   0.320    0.137    0.419 

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: 423
Number of extensions: 21
Number of successful extensions: 3
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: 401
Length of database: 421
Length adjustment: 31
Effective length of query: 370
Effective length of database: 390
Effective search space:   144300
Effective search space used:   144300
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 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