Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate 5208676 Shew_1185 serine hydroxymethyltransferase (RefSeq)
Query= BRENDA::R9YJZ9 (417 letters) >FitnessBrowser__PV4:5208676 Length = 417 Score = 760 bits (1962), Expect = 0.0 Identities = 367/417 (88%), Positives = 400/417 (95%) Query: 1 MLKKAMNIADYDPELFKAIEDETRRQEEHIELIASENYTSPRVMEAQGSQLTNKYAEGYP 60 MLKK MNIAD+DP+LF+AI++ETRRQEEHIELIASENYTSPRVMEAQGSQLTNKYAEGYP Sbjct: 1 MLKKEMNIADFDPQLFQAIQEETRRQEEHIELIASENYTSPRVMEAQGSQLTNKYAEGYP 60 Query: 61 GKRYYGGCEYVDVVETLAIERAKQLFGATYANVQPHSGSQANSAVYMALLQPGDTVLGMN 120 GKRYYGGCE+VD+VE LAIERAK+LFGATYANVQPHSGSQANSAVYMALLQPGDTVLGMN Sbjct: 61 GKRYYGGCEHVDIVENLAIERAKELFGATYANVQPHSGSQANSAVYMALLQPGDTVLGMN 120 Query: 121 LAHGGHLTHGSPVNFSGKLYNIIPYGIDESGKIDYSELETLALEHKPKMIIGGFSAYSGI 180 LAHGGHLTHGSPVNFSGKLYNI+PYGIDESGKIDY E+E LA+EHKPKM+IGGFSAYSGI Sbjct: 121 LAHGGHLTHGSPVNFSGKLYNIVPYGIDESGKIDYDEMERLAVEHKPKMMIGGFSAYSGI 180 Query: 181 VDWAKLREIADKIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTSTTHKTLAGPRGGVIL 240 VDWA++REIADKIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTSTTHKTLAGPRGG+IL Sbjct: 181 VDWARMREIADKIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTSTTHKTLAGPRGGIIL 240 Query: 241 SAADDEDLYKKLNSAVFPGGQGGPLMHVIAGKAVAFKEALEPEFKTYQQQVVNNAKAMVE 300 SAA+DEDLYKKLNSAVFPGGQGGPLMHVIAGKAVAFKEAL PEFK YQQQVV NAKAM Sbjct: 241 SAANDEDLYKKLNSAVFPGGQGGPLMHVIAGKAVAFKEALSPEFKEYQQQVVVNAKAMAN 300 Query: 301 VFLERGYKIVSGGTDNHLMLVDLIGRELTGKEADAALGRANITVNKNSVPNDPRSPFVTS 360 F+ERG+ +VSGGT+NHL L+DLI +++TGK+ADAALGRANITVNKNSVPNDPRSPFVTS Sbjct: 301 TFIERGFDVVSGGTENHLFLLDLIAKDITGKDADAALGRANITVNKNSVPNDPRSPFVTS 360 Query: 361 GVRIGTPAITRRGFKEAEARELTGWICDVLDNAHDDAVIERVKSQVLELCARFPVYG 417 G+RIG+PAITRRGFKEAEA ELT WICDVLD+ +++A IERVK+QVLELCA+FPVYG Sbjct: 361 GLRIGSPAITRRGFKEAEAVELTNWICDVLDDINNEATIERVKNQVLELCAKFPVYG 417 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: 774 Number of extensions: 25 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: 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 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