Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.- (uncharacterized)
to candidate GFF2427 PGA1_c24580 putative serine hydroxymethyltransferase
Query= curated2:Q8TZ19 (428 letters) >FitnessBrowser__Phaeo:GFF2427 Length = 435 Score = 232 bits (592), Expect = 1e-65 Identities = 140/409 (34%), Positives = 215/409 (52%), Gaps = 9/409 (2%) Query: 4 LEDVHSVVRAVEKHHEWLKKCLPMIASENVTSPAVREMLVTDFGHRYAEGKPGERLYEGC 63 L+ + ++V HE + C + + NV +P +L + G R + G PG++ G Sbjct: 33 LDRIATLVEENRVIHE--EDCFNLNPATNVMNPKAEALLASGLGSRPSLGHPGDKYEMGL 90 Query: 64 EYIDEVELACVRLAKELFGAEHANVQPTSGVVANLAALFALTEPGDTILGLRISHGGHIS 123 E I+E+E+ RLA E+F AE + ++ SG +ANL A PGDTI+ S GGH++ Sbjct: 91 EAIEEIEVIAARLACEVFDAEFSEIRVPSGALANLYGFMATCRPGDTIIAPPASIGGHVT 150 Query: 124 HHDISAPGVRGLNVEYLPFDEEDMAIDVDGMVRKIEEVEPSVVMLGASLFLFPHPVEEAV 183 HH G+ GL P E+ +D++ + + E P ++ +G SL LF HPV Sbjct: 151 HHAAGCAGLYGLRSIEAPVLEDGYTVDLEALQQLAERERPKLITIGGSLNLFEHPVAGVR 210 Query: 184 EAVEAVGGYVVYDAAHVLGLIAGGQFQDPIREGAHVVTGSTHKTFPGPQGGIVLC-QRDL 242 + +G V++DAAH G+IAG + DP+ EGAH +T ST+K+ GP GG+++ ++ Sbjct: 211 AIADQIGAKVMFDAAHQCGIIAGKAWADPLAEGAHFMTMSTYKSLGGPAGGLIVSNDAEI 270 Query: 243 ADDIDEAVFPGLVSNHHLHHVAALAVALAEFKEYGERYARDTVRNAKALAEALYAEGLRV 302 A +D FPG+ +N + AALAV L +++++G YA + + AK+LA AL AEGL + Sbjct: 271 AKALDSIAFPGMTANFDVAKSAALAVTLLDWRDHGRAYASEMIAMAKSLAAALEAEGLPL 330 Query: 303 LCEHRGFTESHQIAVDVREQGGGAVIAEKLESANILCNKNLLPWDDESKSHDPSGIRLGT 362 G T SHQ A+ GG ++ L L LP + D +G+R+GT Sbjct: 331 FKTADGITMSHQFALCAAPYCGGQAASKLLRKNGFLACGIGLP--IPAVEGDMNGLRIGT 388 Query: 363 QELTRLGMGLSEMEYIAELIADVVLGRREPSEVRKDVEELRREFQEVKY 411 EL R GM + +A LIA + G V V RR+F + + Sbjct: 389 PELVRWGMTSKDAAALAALIAAALRG----EAVLDRVSAWRRQFDRLHF 433 Lambda K H 0.318 0.137 0.408 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: 409 Number of extensions: 13 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: 428 Length of database: 435 Length adjustment: 32 Effective length of query: 396 Effective length of database: 403 Effective search space: 159588 Effective search space used: 159588 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 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