Align Serine hydroxymethyltransferase; SHMT; Serine methylase; L-threonine/L-allo-threonine aldolase; EC 2.1.2.1; EC 4.1.2.48 (characterized)
to candidate WP_041471486.1 CPHAMN1_RS03155 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_000020545.1:WP_041471486.1 Length = 439 Score = 455 bits (1171), Expect = e-132 Identities = 241/424 (56%), Positives = 295/424 (69%), Gaps = 22/424 (5%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 D I++AI E RQ LELIASENF S AVMEA GSVMTNKYAEG P KRYYGGCEFV Sbjct: 10 DKGIFDAITAEVRRQTETLELIASENFASRAVMEACGSVMTNKYAEGYPGKRYYGGCEFV 69 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 DIAE+LA +RAK LF ++ NVQPHSG+ ANM V AVLKPGD IMG+DLSHGGHLTHG+ Sbjct: 70 DIAENLARDRAKKLFGCDYVNVQPHSGSSANMGVLFAVLKPGDRIMGLDLSHGGHLTHGS 129 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 KVNFSG+++ A YGV ET ID +++ +A E +PKLI+ GASAY + D+ R++A Sbjct: 130 KVNFSGQLFEAHSYGVDRETGCIDMNKVEEMALEVRPKLIICGASAYSQGFDFKAFRDVA 189 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEF----- 242 D VGA+LM D+AH AGLIA G+ +P+P+ HFVT+TTHKTLRGPR G I+ K+F Sbjct: 190 DKVGAFLMADIAHPAGLIAAGLLNDPMPHCHFVTTTTHKTLRGPRGGMIMMGKDFENPLG 249 Query: 243 --------------AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVAN 288 ++ ID + PGIQGGPLMH+IAAK VAF EA+ EFK+YA QV N Sbjct: 250 ITVKTKKGSRTKMMSEVIDAEIMPGIQGGPLMHIIAAKGVAFGEALQPEFKDYAVQVRNN 309 Query: 289 ARVLAEEFIKEGFKVVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPL 348 A V+AE F +++VSGGT +H++L+DLR+ +TG+ E L A ITVNKN VPFD Sbjct: 310 AAVMAERFSGLDYQIVSGGTKNHLMLIDLRNKNVTGKVAENLLHDAGITVNKNMVPFDDK 369 Query: 349 PPVKTSGIRLGTPAMTTRGMKEDQMRIIARLISKVIK---NIGDEKVIEYVRQEVIEMCE 405 P TSGIR+GTPAMTTRGM+E I I +VI + G EKV VR +V MC+ Sbjct: 370 SPFVTSGIRIGTPAMTTRGMQESHAENIVGFIDRVISAADSEGIEKVCAEVRSDVKAMCK 429 Query: 406 QFPL 409 PL Sbjct: 430 DLPL 433 Lambda K H 0.319 0.136 0.395 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: 565 Number of extensions: 34 Number of successful extensions: 3 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: 427 Length of database: 439 Length adjustment: 32 Effective length of query: 395 Effective length of database: 407 Effective search space: 160765 Effective search space used: 160765 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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