Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_041097123.1 SUTH_RS03505 serine hydroxymethyltransferase
Query= BRENDA::B4ECY9 (415 letters) >NCBI__GCF_000828635.1:WP_041097123.1 Length = 414 Score = 639 bits (1648), Expect = 0.0 Identities = 313/409 (76%), Positives = 359/409 (87%) Query: 6 QSTIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGYPGKRY 65 Q+T+A DPE++ AI+ ENRRQEDHIELIASENY S VM AQGSQLTNKYAEGYPGKRY Sbjct: 5 QNTLAKSDPELWTAIQNENRRQEDHIELIASENYVSWPVMEAQGSQLTNKYAEGYPGKRY 64 Query: 66 YGGCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAHG 125 YGGCE VDVVEQLAIDR K+LFGA+AANVQPNSGSQANQ VFFA LKPGDTI+GM+L+ G Sbjct: 65 YGGCENVDVVEQLAIDRAKKLFGADAANVQPNSGSQANQAVFFAFLKPGDTILGMNLSMG 124 Query: 126 GHLTHGSPVNMSGKWFNVVSYGLNENEDIDYDAAEKLANEHKPKLIVAGASAFALKIDFE 185 GHLTHG P+N+SGKWFN+V YGL+ NE+IDY E+LA+EHKPKLI+AGASA+ALKIDFE Sbjct: 125 GHLTHGMPLNISGKWFNIVPYGLDANEEIDYAEMERLAHEHKPKLIIAGASAYALKIDFE 184 Query: 186 RLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKAE 245 R AK+AK+VGA MVDMAHYAGL+AAG YPNPVPHAD VTTTTHK+LRGPRGG+ILM+AE Sbjct: 185 RFAKVAKAVGAIFMVDMAHYAGLVAAGFYPNPVPHADVVTTTTHKTLRGPRGGLILMRAE 244 Query: 246 YEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLVKRGL 305 +EK INS+IFPGIQGGPL HVIAAKAVA KEA++ EFK YQ++V++NA+V+A+ L RGL Sbjct: 245 HEKAINSSIFPGIQGGPLEHVIAAKAVALKEAMTQEFKNYQEQVIDNAQVMAKVLKARGL 304 Query: 306 RIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLGSP 365 RIVSGRTESHV LVDLRAK++TGK AEAALG AH+TVNKN IPNDP+K VTSGIRLG+P Sbjct: 305 RIVSGRTESHVFLVDLRAKNLTGKEAEAALGRAHLTVNKNTIPNDPQKALVTSGIRLGTP 364 Query: 366 AMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVY 414 AMTTRGF EAEQV NLIADVL+ P D A + RVR +V+ L K+FPVY Sbjct: 365 AMTTRGFTEIEAEQVANLIADVLDAPNDEAVLARVRGEVSALCKKFPVY 413 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: 580 Number of extensions: 12 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: 415 Length of database: 414 Length adjustment: 31 Effective length of query: 384 Effective length of database: 383 Effective search space: 147072 Effective search space used: 147072 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