Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_077278481.1 B1C78_RS07180 serine hydroxymethyltransferase
Query= BRENDA::R9YJZ9 (417 letters) >NCBI__GCF_002000365.1:WP_077278481.1 Length = 417 Score = 646 bits (1666), Expect = 0.0 Identities = 319/417 (76%), Positives = 355/417 (85%), Gaps = 1/417 (0%) Query: 1 MLKKAMNIADYDPELFKAIEDETRRQEEHIELIASENYTSPRVMEAQGSQLTNKYAEGYP 60 M M IA YD EL++AIE E RRQEEHIELIASENY SPRVMEAQGS LTNKYAEGYP Sbjct: 1 MFSIQMGIAGYDEELWQAIEGEARRQEEHIELIASENYASPRVMEAQGSVLTNKYAEGYP 60 Query: 61 GKRYYGGCEYVDVVETLAIERAKQLFGATYANVQPHSGSQANSAVYMALLQPGDTVLGMN 120 GKRYYGGCEYVDV E LAIER K+LFGA YANVQPHSGSQAN+AVYMALL PGDTVLGM+ Sbjct: 61 GKRYYGGCEYVDVAERLAIERVKELFGADYANVQPHSGSQANAAVYMALLNPGDTVLGMS 120 Query: 121 LAHGGHLTHGSPVNFSGKLYNIIPYGIDESGKIDYSELETLALEHKPKMIIGGFSAYSGI 180 LAHGGHLTHG+ VNFSGKLYN + YGID+ G ID+ E+E LA+EHKPKMIIGGFSAYS Sbjct: 121 LAHGGHLTHGAKVNFSGKLYNAVQYGIDDEGYIDFDEVERLAVEHKPKMIIGGFSAYSRA 180 Query: 181 VDWAKLREIADKIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTSTTHKTLAGPRGGVIL 240 +DW K R+IADK+GA+L VDMAHVAGL+AAGVYP+PV A V TSTTHKTL GPRGG+IL Sbjct: 181 IDWQKFRDIADKVGAWLLVDMAHVAGLVAAGVYPSPVQIADVTTSTTHKTLRGPRGGIIL 240 Query: 241 SAADDEDLYKKLNSAVFPGGQGGPLMHVIAGKAVAFKEALEPEFKTYQQQVVNNAKAMVE 300 A + D+ KKLNS VFPG QGGPLMHVIA KAVAFKEALEPEFKTYQ+QVV NA+ M Sbjct: 241 -AKSNPDVEKKLNSLVFPGTQGGPLMHVIAAKAVAFKEALEPEFKTYQKQVVANARTMAA 299 Query: 301 VFLERGYKIVSGGTDNHLMLVDLIGRELTGKEADAALGRANITVNKNSVPNDPRSPFVTS 360 +ERGYK+VSGGTDNHL LVDLI + LTGK ADAALG ANITVNKN+VPNDP+SPFVTS Sbjct: 300 TIMERGYKVVSGGTDNHLFLVDLIDKGLTGKAADAALGAANITVNKNAVPNDPQSPFVTS 359 Query: 361 GVRIGTPAITRRGFKEAEARELTGWICDVLDNAHDDAVIERVKSQVLELCARFPVYG 417 G+RIGTPAIT RGF E E+R+L WICDVLD+ + VIE VK++VL++CARFPVYG Sbjct: 360 GIRIGTPAITTRGFGEQESRDLANWICDVLDDHENATVIESVKAKVLDICARFPVYG 416 Lambda K H 0.316 0.135 0.393 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: 638 Number of extensions: 18 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: 417 Length of database: 417 Length adjustment: 31 Effective length of query: 386 Effective length of database: 386 Effective search space: 148996 Effective search space used: 148996 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 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