Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate BPHYT_RS34440 BPHYT_RS34440 serine--glyoxylate aminotransferase
Query= BRENDA::P74281 (384 letters) >FitnessBrowser__BFirm:BPHYT_RS34440 Length = 406 Score = 250 bits (639), Expect = 4e-71 Identities = 138/364 (37%), Positives = 214/364 (58%), Gaps = 7/364 (1%) Query: 4 KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSG 63 + L IPGP+PVP+++L AM+ I HR +F ++ ++ +K + +T+ V++ SG Sbjct: 11 RHFLQIPGPSPVPDRILRAMSYPTIDHRGPEFGELGLKVLDGIKKIFKTQQPVVIYPASG 70 Query: 64 TGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAE----WGKALDPND 119 TGA EA++ N LSPGD VL+ G F W K+A++ GL E + W + + P Sbjct: 71 TGAWEAALSNTLSPGDHVLMFETGHFATLWQKMAESLGLKPEFLGLPGIEGWRRGVQPQM 130 Query: 120 FKTLLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGG-ALMIVDAVTSLGATPV 178 + L AD+ IKA+ + H+ETSTGV +D+AA+ A A G AL++VD ++ L Sbjct: 131 IEERLRADTQHAIKAVCVVHNETSTGVTSDIAAVRRAIDAAGHPALLLVDTISGLACADY 190 Query: 179 AIDDLGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDS 238 D+ G+DV SGSQKG M+PPG+ F ++S KA A + A +PR + D + Sbjct: 191 RHDEWGVDVTVSGSQKGLMLPPGISFNAISPKAVAASKQARLPRSFWDWTDIVEMNKTGY 250 Query: 239 SPFTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPD-NAASN 297 P+TP NL+YGL +L+M+ EGLD +F RH+R ATR A++A L + D + S Sbjct: 251 WPYTPNTNLLYGLNEALEMILGEGLDNVFARHERLAEATRRAVRAWGLEIQCADPSVYSP 310 Query: 298 AITAV-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGAL 356 +T V P G++A+ +R + ++FD+++ G +KG++FRIGHLG D +L+ + Sbjct: 311 VLTGVMMPDGIDADAVRKLIYERFDMSLGTGLGKMKGRMFRIGHLGDCNDLMLLATLAGC 370 Query: 357 EATL 360 E L Sbjct: 371 EMGL 374 Lambda K H 0.317 0.134 0.386 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: 360 Number of extensions: 13 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: 384 Length of database: 406 Length adjustment: 31 Effective length of query: 353 Effective length of database: 375 Effective search space: 132375 Effective search space used: 132375 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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