Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate Pf1N1B4_2161 Serine hydroxymethyltransferase (EC 2.1.2.1)
Query= BRENDA::R9YJZ9 (417 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2161 Length = 421 Score = 590 bits (1521), Expect = e-173 Identities = 291/420 (69%), Positives = 334/420 (79%), Gaps = 4/420 (0%) Query: 1 MLKKAMNIADYDPELFKAIEDETRRQEEHIELIASENYTSPRVMEAQGSQLTNKYAEGYP 60 M + + +D EL +AI +E RQE+H+ELIASENY SP VM+ Q + LTNKYAEGYP Sbjct: 1 MYDSTLTLKAFDAELCEAIHNEEHRQEDHVELIASENYASPLVMKIQSTVLTNKYAEGYP 60 Query: 61 GKRYYGGCEYVDVVETLAIERAKQLFGATYANVQPHSGSQANSAVYMALLQPGDTVLGMN 120 GKRYY GCEYVDV E LAIER K LF YANVQPH+G+QAN+AV++AL+ PGDTV+GMN Sbjct: 61 GKRYYSGCEYVDVAERLAIERVKALFNCDYANVQPHAGAQANAAVFLALINPGDTVMGMN 120 Query: 121 LAHGGHLTHGSPVNFSGKLYNIIPYGID-ESGKIDYSELETLALEHKPKMIIGGFSAYSG 179 LA GGHLTHG+P NFSG+ Y I+PYG+D E+G +DY E+E +ALE +PKM+IGGFSAYS Sbjct: 121 LAQGGHLTHGNPSNFSGRHYKIVPYGLDPETGFLDYDEMERIALETRPKMLIGGFSAYSR 180 Query: 180 IVDWAKLREIADKIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTSTTHKTLAGPRGGVI 239 DWA++R IADK+GA +VDMAHVAGLIAAG YP+P+PHAHVVTSTTHKTL GPRGG+I Sbjct: 181 YKDWARMRAIADKVGAIFWVDMAHVAGLIAAGEYPDPLPHAHVVTSTTHKTLRGPRGGLI 240 Query: 240 LSAADDEDLYKKLNSAVFPGGQGGPLMHVIAGKAVAFKEALEPEFKTYQQQVVNNAKAMV 299 LS DE YKKL+SAVFPG QGGPLMH IA KAVAFKEAL PEFKTYQ QVV NA+AM Sbjct: 241 LSKGQDEAFYKKLDSAVFPGVQGGPLMHQIAAKAVAFKEALRPEFKTYQTQVVINARAMA 300 Query: 300 EVFLERGYKIVSGGTDNHLMLVDLIGRELTGKEADAALGRANITVNKNSVPNDPRSPFVT 359 V ERGYKIVSGGTDNH+ML+DL R TGKEADAAL A IT NKNSVPNDPRSPFVT Sbjct: 301 AVLQERGYKIVSGGTDNHMMLIDLSDRPYTGKEADAALSNAYITANKNSVPNDPRSPFVT 360 Query: 360 SGVRIGTPAITRRGFKEAEARELTGWICDVLD---NAHDDAVIERVKSQVLELCARFPVY 416 SG+RIGTPAIT RGF E +L GW+CDVLD N + V V+ QV+ELC R PVY Sbjct: 361 SGLRIGTPAITTRGFGVIECEQLAGWLCDVLDALENGDSERVGHHVREQVVELCRRHPVY 420 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: 633 Number of extensions: 28 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: 417 Length of database: 421 Length adjustment: 32 Effective length of query: 385 Effective length of database: 389 Effective search space: 149765 Effective search space used: 149765 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