Align asparagine-oxo-acid transaminase (EC 2.6.1.14); alanine-glyoxylate transaminase (EC 2.6.1.44); serine-glyoxylate transaminase (EC 2.6.1.45) (characterized)
to candidate SMa2139 SMa2139 SgaA serine-glyoxylate aminotransferase (SGAT)
Query= BRENDA::Q56YA5 (401 letters) >FitnessBrowser__Smeli:SMa2139 Length = 401 Score = 400 bits (1028), Expect = e-116 Identities = 198/389 (50%), Positives = 267/389 (68%), Gaps = 1/389 (0%) Query: 8 GRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPT 67 G HLFVPGP NIP+ V RAMN +D R+P P L L D+K +F+T +G+ FLFP Sbjct: 4 GTSHLFVPGPTNIPDAVRRAMNVPMQDMRAPDFPDLVLPLFADLKGVFRTDNGSIFLFPG 63 Query: 68 TGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLA 127 +GTGAWE+A++NTL+ GDR++ GQFS LW D RL +V+ ++ +WG+G ++ Sbjct: 64 SGTGAWEAAISNTLNRGDRVLMSRFGQFSHLWADMAGRLGLDVECLDVEWGEGVPVEEYR 123 Query: 128 SKLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRM 187 +L D+N IKA+ + HNETATGVT+D++AVR LD H ALL VDGVSSI +++FRM Sbjct: 124 RRLDADKNRRIKAVFVTHNETATGVTSDVAAVRAALDDTGHKALLFVDGVSSIASIEFRM 183 Query: 188 DEWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTYW 247 D+WGVD+A+TGSQK L LP GLGI+ SPKALEA +S + +F + D + G Y+ Sbjct: 184 DDWGVDLAVTGSQKGLMLPAGLGILAVSPKALEAHASSTIERCYFSFEDMKAPSETG-YF 242 Query: 248 PYTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKEEWISNT 307 PYTP QLL GLRA+LDLIF EGL+ +IARH RL + R V AWGL C +++W S+T Sbjct: 243 PYTPPTQLLLGLRASLDLIFAEGLDAVIARHHRLAEGVRRGVHAWGLNLCATEKKWWSDT 302 Query: 308 VTAVMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCLAGVE 367 V+A++VP +D +++ + +Y S G GL+KVAG+VFRIGHLG++NE+ L LA E Sbjct: 303 VSAIVVPEDVDARQVIANGYSKYRTSFGAGLSKVAGRVFRIGHLGDLNEVMCLSALAAAE 362 Query: 368 MILKDVGYPVVMGSGVAAASTYLQHHIPL 396 M L+D G + GSGVAAA + + I L Sbjct: 363 MSLRDAGAKIEAGSGVAAAQEWYRSQIGL 391 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: 426 Number of extensions: 14 Number of successful extensions: 2 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: 401 Length adjustment: 31 Effective length of query: 370 Effective length of database: 370 Effective search space: 136900 Effective search space used: 136900 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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