Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_014149648.1 MEALZ_RS15735 serine hydroxymethyltransferase
Query= BRENDA::L7Y8B0 (417 letters) >NCBI__GCF_000968535.2:WP_014149648.1 Length = 417 Score = 629 bits (1621), Expect = 0.0 Identities = 308/416 (74%), Positives = 357/416 (85%) Query: 1 MFSKQDQIQGYDDALLAAMNAEEQRQEDHIELIASENYTSKRVMQAQGSGLTNKYAEGYP 60 MF+K I GYD+ L A+ E +RQEDHIELIASENYTS RVM+AQG+ LTNKYAEGYP Sbjct: 1 MFTKSQTIAGYDNELFQALEEERRRQEDHIELIASENYTSPRVMEAQGTLLTNKYAEGYP 60 Query: 61 GKRYYGGCEHVDKVEALAIERAKQLFGADYANVQPHSGSSANGAVYLALVQAGDTILGMS 120 GKRYYGGCE+VDKVE LAI+RAK+LFGADYANVQ HSGS AN AV++AL+Q GDTILG+S Sbjct: 61 GKRYYGGCEYVDKVEQLAIDRAKELFGADYANVQAHSGSQANMAVFMALIQPGDTILGLS 120 Query: 121 LAHGGHLTHGAKVSSSGKLYNAVQYGIDTNTGLIDYDEVERLAVEHKPKMIVAGFSAYSK 180 LA GGHLTHGAK + SGK+YNAVQYG+ +TGLIDYD+VE LA+EHKPK++VAGFSAYS+ Sbjct: 121 LADGGHLTHGAKPNFSGKIYNAVQYGLHPDTGLIDYDQVEALAIEHKPKVLVAGFSAYSR 180 Query: 181 TLDFPRFRAIADKVGALLFVDMAHVAGLVAAGLYPNPIPFADVVTTTTHKTLRGPRGGLI 240 D+ RFR IADKVGA L VDMAHVAGLVAAGLYPNP+PFADVVT+TTHK+LRGPRGGLI Sbjct: 181 IWDWQRFREIADKVGAYLLVDMAHVAGLVAAGLYPNPVPFADVVTSTTHKSLRGPRGGLI 240 Query: 241 LAKANEEIEKKLNAAVFPGAQGGPLMHVIAAKAVCFKEALEPEFKAYQQQVIENAQAMAQ 300 L K+N EIEKK ++++FPG QGGP MHVIAAKAV FKEA+E EFK YQQQVI NA+AMA+ Sbjct: 241 LCKSNPEIEKKFDSSIFPGIQGGPSMHVIAAKAVAFKEAMETEFKTYQQQVINNAKAMAE 300 Query: 301 VFVDRGYDVVSGGTDNHLFLVSLIRQGLTGKDADAALGCAHITVNKNAVPNDPQSPFVTS 360 VF+DRG+DVVSGGTDNHL LVSLI +G+TGK ADAALG AHITVNKNAVPNDPQSPFVTS Sbjct: 301 VFIDRGFDVVSGGTDNHLMLVSLIPKGITGKAADAALGRAHITVNKNAVPNDPQSPFVTS 360 Query: 361 GLRIGTPAVTTRGFKVAQCVALAGWICDILDNLGDADVEADVAKNVAALCADFPVY 416 G+R+GTPA TTRGFK AQ +A +CD+++N+ + V + V VA LC+ FPVY Sbjct: 361 GIRVGTPAPTTRGFKEAQMTEIAHLMCDVMENIDNESVISAVRDKVAILCSRFPVY 416 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: 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 (21.7 bits) S2: 50 (23.9 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