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 WP_012405153.1 BPHY_RS29640 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::Q56YA5 (401 letters) >NCBI__GCF_000020045.1:WP_012405153.1 Length = 421 Score = 438 bits (1126), Expect = e-127 Identities = 216/389 (55%), Positives = 282/389 (72%), Gaps = 2/389 (0%) Query: 8 GRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPT 67 GR+ L VPGP N+P+ V+RAM + ED+RS P L LL D+KKI++T G PF+FP+ Sbjct: 11 GRNILAVPGPTNVPDAVLRAMVVSMEDHRSTKFPELAHGLLSDLKKIYRTAEGQPFIFPS 70 Query: 68 TGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLA 127 +GTGAWE+ALTNTLSPGDR++ GQFS LW D +RL F+V++++ DWG+G ++ +A Sbjct: 71 SGTGAWEAALTNTLSPGDRVLVPRFGQFSHLWADMAQRLGFDVEILDVDWGEGVPVERIA 130 Query: 128 SKLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRM 187 L D HTIK I HNETATGVT+DI A+R +D +HPALL VDGVSSI +DFRM Sbjct: 131 EILKADGQHTIKGILACHNETATGVTSDIGALRRAMDDARHPALLFVDGVSSIGCIDFRM 190 Query: 188 DEWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTYW 247 DEWGVD+A+TGSQK L LP GLGI+C S KAL+A +KS + +FD D ++ G Y+ Sbjct: 191 DEWGVDLAVTGSQKGLMLPAGLGILCVSQKALKAISHAKSRRCYFDLADMVRTNATG-YF 249 Query: 248 PYTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAV-EAWGLKNCTQKEEWISN 306 PYTP++ LLYGLRAALDL+FEEGLEN+ ARH L R AV E WGL+ C + W S+ Sbjct: 250 PYTPALSLLYGLRAALDLLFEEGLENVFARHHYLAAGVRAAVTEGWGLELCAKAPRWHSD 309 Query: 307 TVTAVMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCLAGV 366 TV+A++VP ++ ++++ A++RYNL+LG GL+KVAGKVFRIGHLG++NEL L+ +AG Sbjct: 310 TVSAIVVPEGVNAAQVIDTAYRRYNLALGAGLSKVAGKVFRIGHLGDLNELMLMSAIAGA 369 Query: 367 EMILKDVGYPVVMGSGVAAASTYLQHHIP 395 EM + D G V GSGV AA Y + H P Sbjct: 370 EMAMLDAGIDVRPGSGVGAAGQYWRTHTP 398 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: 489 Number of extensions: 13 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 Apr 10 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