Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_029909421.1 P166_RS0105200 serine hydroxymethyltransferase
Query= BRENDA::L7Y8B0 (417 letters) >NCBI__GCF_000711315.1:WP_029909421.1 Length = 431 Score = 617 bits (1592), Expect = 0.0 Identities = 311/422 (73%), Positives = 346/422 (81%), Gaps = 6/422 (1%) Query: 1 MFSKQDQIQGYDDALLAAMNAEEQRQEDHIELIASENYTSKRVMQAQGSGLTNKYAEGYP 60 MF K I GYDD L A+ +E QRQEDHIELIASENYTS RVM+AQGS LTNKYAEGYP Sbjct: 1 MFDKSMTIAGYDDVLADAIKSEAQRQEDHIELIASENYTSPRVMEAQGSVLTNKYAEGYP 60 Query: 61 GKRYYGGCEHVDKVEALAIERAKQLFGADYANVQPHSGSSANGAVYLALVQAGDTILGMS 120 GKRYYGGCE VD VE LAI+RAK+LFGADYANVQPHSGS AN VY+AL++ GDT+LGMS Sbjct: 61 GKRYYGGCEFVDVVEQLAIDRAKELFGADYANVQPHSGSQANAPVYMALLEPGDTVLGMS 120 Query: 121 LAHGGHLTHGAKVSSSGKLYNAVQYGIDTNTGLIDYDEVERLAVEHKPKMIVAGFSAYSK 180 LAHGGHLTHG+ VS SGK+YNAVQYG++ TG IDY+EVERLA EHKPKMI+AGFSAYS+ Sbjct: 121 LAHGGHLTHGSHVSFSGKIYNAVQYGLNPETGEIDYEEVERLAKEHKPKMIIAGFSAYSQ 180 Query: 181 TLDFPRFRAIADKVGALLFVDMAHVAGLVAAGLYPNPIPFADVVTTTTHKTLRGPRGGLI 240 +D+ RFR IAD VGA L VDMAHVAGLVA G YPNP+ ADV TTTTHKTLRGPR GLI Sbjct: 181 VVDWQRFRDIADMVGAYLMVDMAHVAGLVAVGEYPNPVQIADVTTTTTHKTLRGPRSGLI 240 Query: 241 LAKANEEIEKKLNAAVFPGAQGGPLMHVIAAKAVCFKEALEPEFKAYQQQVIENAQAMAQ 300 LAKAN EIEKKLN+A+FPGAQGGPLMHVIAAKAV FKEA+EPEFK Y Q V NA+AMA+ Sbjct: 241 LAKANPEIEKKLNSAIFPGAQGGPLMHVIAAKAVAFKEAMEPEFKTYIQNVKANAKAMAK 300 Query: 301 VFVDRGYDVVSGGTDNHLFLVSLIRQGLTGKDADAALGCAHITVNKNAVPNDPQSPFVTS 360 VF+DRGYDVVS GT+NHLFLVS I+QGLTGK DAAL AHITVNKN+VPNDP SPFVTS Sbjct: 301 VFMDRGYDVVSKGTENHLFLVSFIQQGLTGKLVDAALDAAHITVNKNSVPNDPMSPFVTS 360 Query: 361 GLRIGTPAVTTRGFKVAQCVALAGWICDILDNLG------DADVEADVAKNVAALCADFP 414 G+RIGT A TTRGF V LA W+CD++D+ D +V V + V ALCAD P Sbjct: 361 GIRIGTAASTTRGFTVEDSTNLANWMCDVIDSCSQDDGTWDEEVVDQVRQKVEALCADRP 420 Query: 415 VY 416 VY Sbjct: 421 VY 422 Lambda K H 0.318 0.134 0.390 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: 625 Number of extensions: 23 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: 431 Length adjustment: 32 Effective length of query: 385 Effective length of database: 399 Effective search space: 153615 Effective search space used: 153615 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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