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.
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:
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