Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate Pf6N2E2_5295 Serine hydroxymethyltransferase (EC 2.1.2.1)
Query= BRENDA::B4ECY9 (415 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5295 Length = 412 Score = 540 bits (1392), Expect = e-158 Identities = 263/408 (64%), Positives = 326/408 (79%), Gaps = 1/408 (0%) Query: 8 TIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGYPGKRYYG 67 ++ N DP + I++E RQE H+ELIASENY S V+ AQGS LTNKYAEGYPGKRYYG Sbjct: 2 SLQNFDPTLARLIDRERNRQETHLELIASENYVSEEVLQAQGSVLTNKYAEGYPGKRYYG 61 Query: 68 GCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAHGGH 127 GC+ VD +E LAI+R ++LF E NVQP+SGSQANQ VF A+L+PGDTI+GMSLAHGGH Sbjct: 62 GCKVVDEIENLAIERARKLFNCEYVNVQPHSGSQANQAVFLAVLEPGDTILGMSLAHGGH 121 Query: 128 LTHGSPVNMSGKWFNVVSYGLN-ENEDIDYDAAEKLANEHKPKLIVAGASAFALKIDFER 186 LTHG+ VN SGK + SYGL+ E E +DY+ E LA EH+PK+I+AGASA++ IDF+R Sbjct: 122 LTHGASVNFSGKIYRAFSYGLDTETETLDYEEMEALAREHRPKMIIAGASAYSRTIDFQR 181 Query: 187 LAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKAEY 246 KI +GAYLMVDMAHYAGLIAAGVYP+PV ADF+T+TTHK+LRGPRGG+IL KA+Y Sbjct: 182 FRKICDEIGAYLMVDMAHYAGLIAAGVYPSPVGIADFITSTTHKTLRGPRGGLILAKAQY 241 Query: 247 EKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLVKRGLR 306 ++ IFP QGGPLMHVIAAKAVAF EAL FK YQQ+V++NARV+A+ L +RGLR Sbjct: 242 GALLDKTIFPVYQGGPLMHVIAAKAVAFNEALGDGFKHYQQRVIDNARVMADVLTRRGLR 301 Query: 307 IVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLGSPA 366 +VSG T+ H+ L+DLR+ +ITGK AEA L +AHIT+NKNAIPNDP+KP +TSGIR+G+PA Sbjct: 302 VVSGGTDCHMFLLDLRSMNITGKDAEALLESAHITLNKNAIPNDPQKPAITSGIRIGTPA 361 Query: 367 MTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVY 414 +TTRGFG AE +V NLIAD+LE P++AA ++ R +V L + FPVY Sbjct: 362 LTTRGFGEAECAEVANLIADLLEQPDNAARLDNTRRRVMHLCECFPVY 409 Lambda K H 0.316 0.132 0.376 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: 519 Number of extensions: 13 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: 415 Length of database: 412 Length adjustment: 31 Effective length of query: 384 Effective length of database: 381 Effective search space: 146304 Effective search space used: 146304 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