Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1 (characterized)
to candidate WP_010531577.1 ON01_RS13415 serine hydroxymethyltransferase
Query= SwissProt::P39148 (415 letters) >NCBI__GCF_000224785.1:WP_010531577.1 Length = 411 Score = 619 bits (1596), Expect = 0.0 Identities = 301/410 (73%), Positives = 348/410 (84%) Query: 1 MKHLPAQDEQVFNAIKNERERQQTKIELIASENFVSEAVMEAQGSVLTNKYAEGYPGKRY 60 M HL D +VF AI++E+ RQQ KIELIASENFVSEAVMEA GSV+TNKYAEGYP KRY Sbjct: 1 MDHLKQTDHEVFEAIQDEKTRQQDKIELIASENFVSEAVMEAMGSVMTNKYAEGYPSKRY 60 Query: 61 YGGCEHVDVVEDIARDRAKEIFGAEHVNVQPHSGAQANMAVYFTILEQGDTVLGMNLSHG 120 YGGCEHVDVVE++ARDRAKE+FGA+H NVQPHSGAQANMAVYF++L GDT+LGMNL+HG Sbjct: 61 YGGCEHVDVVENLARDRAKELFGADHANVQPHSGAQANMAVYFSVLNPGDTILGMNLNHG 120 Query: 121 GHLTHGSPVNFSGVQYNFVEYGVDKETQYIDYDDVREKALAHKPKLIVAGASAYPRTIDF 180 GHLTHGSPVNFSG YN V+YGVD ET+ +DYD V E+A +PKLI+AGASAY R IDF Sbjct: 121 GHLTHGSPVNFSGKLYNVVDYGVDDETEKLDYDAVLERAKEEQPKLIIAGASAYSREIDF 180 Query: 181 KKFREIADEVGAYFMVDMAHIAGLVAAGLHPNPVPYADFVTTTTHKTLRGPRGGMILCRE 240 KFREIADEVGAY +VDMAHIAGLVAAGLH NPV +ADFVTTTTHKTLRGPRGGMILC+E Sbjct: 181 SKFREIADEVGAYLLVDMAHIAGLVAAGLHQNPVEHADFVTTTTHKTLRGPRGGMILCKE 240 Query: 241 EFGKKIDKSIFPGIQGGPLMHVIAAKAVSFGEVLQDDFKTYAQNVISNAKRLAEALTKEG 300 E K IDK++FP +QGGPLMHVIAAKAVSF E L DDFKTYA+ +I NAK L++ALT EG Sbjct: 241 EHAKLIDKNVFPRMQGGPLMHVIAAKAVSFKEALTDDFKTYAKQIIQNAKALSDALTNEG 300 Query: 301 IQLVSGGTDNHLILVDLRSLGLTGKVAEHVLDEIGITSNKNAIPYDPEKPFVTSGIRLGT 360 +++VSGGTDNHL+L+D+ L LTGKVAE+VLD IGIT+NKN IP+D E PFVTSG+R+GT Sbjct: 301 LRVVSGGTDNHLLLLDVTPLNLTGKVAENVLDNIGITANKNTIPFDQESPFVTSGMRMGT 360 Query: 361 AAVTSRGFDGDALEEVGAIIALALKNHEDEGKLEEARQRVAALTDKFPLY 410 AAVT+RGF ++E+ +IIAL LKNHEDE L EA +RV LT F +Y Sbjct: 361 AAVTTRGFKEPEMKEIASIIALVLKNHEDENVLREAEERVQTLTGNFAIY 410 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: 632 Number of extensions: 20 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: 411 Length adjustment: 31 Effective length of query: 384 Effective length of database: 380 Effective search space: 145920 Effective search space used: 145920 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 Jul 26 2024. The underlying query database was built on Jul 25 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