Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate CA265_RS19165 CA265_RS19165 serine hydroxymethyltransferase
Query= BRENDA::R9YJZ9 (417 letters) >FitnessBrowser__Pedo557:CA265_RS19165 Length = 423 Score = 484 bits (1245), Expect = e-141 Identities = 243/419 (57%), Positives = 311/419 (74%), Gaps = 14/419 (3%) Query: 12 DPELFKAIEDETRRQEEHIELIASENYTSPRVMEAQGSQLTNKYAEGYPGKRYYGGCEYV 71 D ++F+ I+ E RQE +ELIASEN+ S +VMEA GS LTNKYAEG PGKRYYGGC+ V Sbjct: 4 DNQIFELIDKELNRQEHGLELIASENFVSKQVMEAAGSVLTNKYAEGLPGKRYYGGCQVV 63 Query: 72 DVVETLAIERAKQLFGATYANVQPHSGSQANSAVYMALLQPGDTVLGMNLAHGGHLTHGS 131 DVVE +AI+RAK+LFGA + NVQPHSG+QAN+AV +A+LQPGD +LG +L+HGGHLTHGS Sbjct: 64 DVVEQIAIDRAKELFGAAWVNVQPHSGAQANAAVMLAILQPGDKILGFDLSHGGHLTHGS 123 Query: 132 PVNFSGKLYNIIPYGID-ESGKIDYSELETLALEHKPKMIIGGFSAYSGIVDWAKLREIA 190 PVNFSGKLY + YG++ E+G IDY +LE +AL KPK+II G SAYS D+A +R +A Sbjct: 124 PVNFSGKLYQPLFYGVEKETGLIDYKKLEEVALAEKPKLIICGASAYSREWDYAFIRSVA 183 Query: 191 DKIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTSTTHKTLAGPRGGVILSAADDED--- 247 DKIGA + D++H AGLIA G+ NP+PH H+VT+TTHKTL GPRGG+I+ D E+ Sbjct: 184 DKIGALVLADISHPAGLIAKGLLANPLPHCHIVTTTTHKTLRGPRGGMIMMGQDFENPWG 243 Query: 248 ----------LYKKLNSAVFPGGQGGPLMHVIAGKAVAFKEALEPEFKTYQQQVVNNAKA 297 + L+ AVFPG QGGPL H+IA KA+AF EAL E+ TY +QV NA+A Sbjct: 244 LKTPKGEIRLMSNLLDMAVFPGTQGGPLEHIIAAKAIAFGEALSEEYGTYIKQVAANAQA 303 Query: 298 MVEVFLERGYKIVSGGTDNHLMLVDLIGRELTGKEADAALGRANITVNKNSVPNDPRSPF 357 M + F+ +GY I+SGGTDNHLML+DL + +TGK A+ AL +A ITVNKN VP D +SPF Sbjct: 304 MAKAFVAKGYGIISGGTDNHLMLIDLRNKNITGKVAENALEKAEITVNKNMVPFDDKSPF 363 Query: 358 VTSGVRIGTPAITRRGFKEAEARELTGWICDVLDNAHDDAVIERVKSQVLELCARFPVY 416 VTSG+R+GT AIT RG KE E ++ I VL N D+A + VK++V++L + FP+Y Sbjct: 364 VTSGIRVGTAAITTRGLKETEMEKIVDLIDQVLTNPEDEANLNSVKAEVIKLVSAFPLY 422 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: 549 Number of extensions: 23 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: 417 Length of database: 423 Length adjustment: 32 Effective length of query: 385 Effective length of database: 391 Effective search space: 150535 Effective search space used: 150535 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