Align glycine hydroxymethyltransferase (EC 2.1.2.1); low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate Pf1N1B4_2778 Serine hydroxymethyltransferase (EC 2.1.2.1)
Query= BRENDA::P0A825 (417 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2778 Length = 417 Score = 630 bits (1626), Expect = 0.0 Identities = 306/416 (73%), Positives = 357/416 (85%), Gaps = 1/416 (0%) Query: 1 MLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYP 60 M R++ IA YDA+L+ AMEQE RQEEHIELIASENYTSP VM+AQGS LTNKYAEGYP Sbjct: 1 MFSRDLTIAKYDADLFAAMEQEAQRQEEHIELIASENYTSPAVMEAQGSVLTNKYAEGYP 60 Query: 61 GKRYYGGCEYVDIVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLEPGDTVLGMN 120 GKRYYGGCE+VD+VEQLAIDRAKELFGADYANVQPH+GSQAN AVY ALL+ GDT+LGM+ Sbjct: 61 GKRYYGGCEFVDVVEQLAIDRAKELFGADYANVQPHAGSQANSAVYLALLQAGDTILGMS 120 Query: 121 LAHGGHLTHGSPVNFSGKLYNIVPYGIDATGHIDYADLEKQAKEHKPKMIIGGFSAYSGV 180 LAHGGHLTHG+ V+ SGKLYN V YGIDA G IDY ++E+ A EHKPKMI+ GFSAYS + Sbjct: 121 LAHGGHLTHGASVSSSGKLYNAVQYGIDANGLIDYDEVERLAVEHKPKMIVAGFSAYSQI 180 Query: 181 VDWAKMREIADSIGAYLFVDMAHVAGLVAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLIL 240 +D+ + REIAD +GAYLFVDMAHVAGLVAAGVYPNPVP A VVTTTTHKTL GPRGGLIL Sbjct: 181 LDFPRFREIADKVGAYLFVDMAHVAGLVAAGVYPNPVPFADVVTTTTHKTLRGPRGGLIL 240 Query: 241 AKGGSEELYKKLNSAVFPGGQGGPLMHVIAGKAVALKEAMEPEFKTYQQQVAKNAKAMVE 300 A+ + ++ KKLNSAVFPG QGGPL HVIA KA+ KEA++PEFK YQQQV KNA+AM Sbjct: 241 ARANA-DIEKKLNSAVFPGAQGGPLEHVIAAKAICFKEALQPEFKAYQQQVVKNAQAMAG 299 Query: 301 VFLERGYKVVSGGTDNHLFLVDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTS 360 VF+ERG+ VVSGGT NHLFL+ L+ + ++GK+ADAALG+A ITVNKNSVPNDP+SPFVTS Sbjct: 300 VFIERGFDVVSGGTQNHLFLLSLIKQEISGKDADAALGKAFITVNKNSVPNDPRSPFVTS 359 Query: 361 GIRVGTPAITRRGFKEAEAKELAGWMCDVLDSINDEAVIERIKGKVLDICARYPVY 416 G+R GTPA+T RGFKEAE KELAGW+CD+L +++EAVI+ ++ KV IC + PVY Sbjct: 360 GLRFGTPAVTTRGFKEAECKELAGWICDILADLSNEAVIDAVREKVKAICKKLPVY 415 Lambda K H 0.316 0.134 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: 651 Number of extensions: 20 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 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