Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1 (characterized)
to candidate WP_028585611.1 G494_RS0117855 serine hydroxymethyltransferase
Query= SwissProt::P39148 (415 letters) >NCBI__GCF_000429965.1:WP_028585611.1 Length = 418 Score = 465 bits (1197), Expect = e-135 Identities = 230/408 (56%), Positives = 293/408 (71%) Query: 1 MKHLPAQDEQVFNAIKNERERQQTKIELIASENFVSEAVMEAQGSVLTNKYAEGYPGKRY 60 M +L QD+++++ I+ E +RQ KI LIASEN+VS AVMEA GSV TNKY+EGY GKRY Sbjct: 1 MNNLQQQDQEIYDLIQQEEQRQADKIRLIASENYVSSAVMEATGSVFTNKYSEGYAGKRY 60 Query: 61 YGGCEHVDVVEDIARDRAKEIFGAEHVNVQPHSGAQANMAVYFTILEQGDTVLGMNLSHG 120 Y G ++VD VE +A RAK++FGA+HVNVQP+SG+ AN+AVY ++ GDT+LGM L HG Sbjct: 61 YEGQQYVDQVELLAIQRAKDLFGADHVNVQPYSGSPANLAVYLAFIKPGDTILGMALPHG 120 Query: 121 GHLTHGSPVNFSGVQYNFVEYGVDKETQYIDYDDVREKALAHKPKLIVAGASAYPRTIDF 180 GHLTHGS V+ SG +N Y +D+ET +DYD +R KA A KPK+++AG SA+ R +DF Sbjct: 121 GHLTHGSKVSISGKYFNAESYSLDQETGTLDYDAIRAKAKACKPKILIAGHSAFSRVLDF 180 Query: 181 KKFREIADEVGAYFMVDMAHIAGLVAAGLHPNPVPYADFVTTTTHKTLRGPRGGMILCRE 240 +FR+IADEV A +VDMAH AGLVA G HP+P+PYAD VTTTTHK+LRGPRG MILC+E Sbjct: 181 AEFRKIADEVNALLLVDMAHFAGLVAGGAHPSPIPYADVVTTTTHKSLRGPRGAMILCKE 240 Query: 241 EFGKKIDKSIFPGIQGGPLMHVIAAKAVSFGEVLQDDFKTYAQNVISNAKRLAEALTKEG 300 E + IDK++FPGIQGGP AA AV+ E FK YA +++NAK LA L ++G Sbjct: 241 EHAQAIDKAVFPGIQGGPHNSTTAAIAVALKEAASPAFKEYAAQIVANAKTLATTLNEQG 300 Query: 301 IQLVSGGTDNHLILVDLRSLGLTGKVAEHVLDEIGITSNKNAIPYDPEKPFVTSGIRLGT 360 LV+GGTDNHL+L+DL + G+TGKVA LD GI N NA+P+DP KPF SG+RLGT Sbjct: 301 FHLVTGGTDNHLLLIDLTNKGVTGKVAAKALDAAGIVLNYNAVPFDPRKPFDPSGVRLGT 360 Query: 361 AAVTSRGFDGDALEEVGAIIALALKNHEDEGKLEEARQRVAALTDKFP 408 +AVTSRGF + ++G I + ED+ E Q V L FP Sbjct: 361 SAVTSRGFKEAEMVKIGNWINAIVSAPEDQALQAETAQAVKDLCAAFP 408 Lambda K H 0.317 0.136 0.388 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: 541 Number of extensions: 18 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: 418 Length adjustment: 31 Effective length of query: 384 Effective length of database: 387 Effective search space: 148608 Effective search space used: 148608 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 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