Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate BPHYT_RS03725 BPHYT_RS03725 serine hydroxymethyltransferase
Query= BRENDA::B4ECY9 (415 letters) >FitnessBrowser__BFirm:BPHYT_RS03725 Length = 415 Score = 776 bits (2003), Expect = 0.0 Identities = 390/415 (93%), Positives = 402/415 (96%) Query: 1 MFDRAQSTIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGY 60 MFDRAQSTIANVDPE++ IEQENRRQE+HIELIASENYTSPAVMAAQGSQLTNKYAEGY Sbjct: 1 MFDRAQSTIANVDPELWKVIEQENRRQEEHIELIASENYTSPAVMAAQGSQLTNKYAEGY 60 Query: 61 PGKRYYGGCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGM 120 PGKRYYGGCEYVDV EQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGM Sbjct: 61 PGKRYYGGCEYVDVAEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGM 120 Query: 121 SLAHGGHLTHGSPVNMSGKWFNVVSYGLNENEDIDYDAAEKLANEHKPKLIVAGASAFAL 180 SLAHGGHLTHGSPVNMSGKWFNVVSYGLNE EDIDYDAAEKLA EHKPKLIVAGASAF+L Sbjct: 121 SLAHGGHLTHGSPVNMSGKWFNVVSYGLNEAEDIDYDAAEKLAQEHKPKLIVAGASAFSL 180 Query: 181 KIDFERLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVI 240 +IDFER++KIAKSVGAY MVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVI Sbjct: 181 RIDFERMSKIAKSVGAYFMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVI 240 Query: 241 LMKAEYEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETL 300 LMKAE+EK INSAIFPGIQGGPLMHVIA KAVAFKEALSPEFK YQQ+VVENARVLAETL Sbjct: 241 LMKAEFEKQINSAIFPGIQGGPLMHVIAGKAVAFKEALSPEFKAYQQQVVENARVLAETL 300 Query: 301 VKRGLRIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGI 360 VKRGLRIVSGRTESHVMLVDLRAK ITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSG+ Sbjct: 301 VKRGLRIVSGRTESHVMLVDLRAKKITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGV 360 Query: 361 RLGSPAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVYR 415 RLGSPAMTTRGFG EAEQVGNLIADVL+NPEDAATIERVR QVAELT+RFPVYR Sbjct: 361 RLGSPAMTTRGFGVKEAEQVGNLIADVLDNPEDAATIERVRGQVAELTQRFPVYR 415 Lambda K H 0.316 0.132 0.376 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: 681 Number of extensions: 15 Number of successful extensions: 1 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: 415 Length of database: 415 Length adjustment: 31 Effective length of query: 384 Effective length of database: 384 Effective search space: 147456 Effective search space used: 147456 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 (21.6 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