Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.- (uncharacterized)
to candidate BPHYT_RS01260 BPHYT_RS01260 hypothetical protein
Query= curated2:Q8TZ19 (428 letters) >FitnessBrowser__BFirm:BPHYT_RS01260 Length = 376 Score = 291 bits (745), Expect = 2e-83 Identities = 163/368 (44%), Positives = 219/368 (59%), Gaps = 4/368 (1%) Query: 47 GHRYAEGKPGE--RLYEGCEYIDEVELACVRLAKELFGAEHANVQPTSGVVANLAALFAL 104 G R + G G R + G +IDE+E CV L K+ F +A+ + G+ A L A AL Sbjct: 1 GTRASGGHIGRDNRFFAGMRFIDELESLCVELLKKAFRVRYADHRLMGGMAATLVAYTAL 60 Query: 105 TEPGDTILGLRISHGGHISHHDISAPGVRGLNVEYLPFDEEDMAIDVDGMVRKIEEVEPS 164 T+PGD ++ + GG S+ PGVRG V +P+ +D +I++D + P+ Sbjct: 61 TQPGDRVMTAPLQMGGDTSNRTNGPPGVRGTRVIDIPYSVKDGSINLDEFATIARKERPA 120 Query: 165 VVMLGASLFLFPHPVEEAVEAVEAVGGYVVYDAAHVLGLIAGGQFQDPIREGAHVVTGST 224 V LG +L LFP P+ E V GG V +D AH LGLI+ G FQDP+ EGA V+TGS+ Sbjct: 121 VTGLGMTLTLFPLPIREIKAIVSEWGGLVYFDGAHQLGLISAGLFQDPLGEGADVMTGSS 180 Query: 225 HKTFPGPQGGIVLCQRD-LADDIDEAVFPGLVSNHHLHHVAALAVALAEFKEYGERYARD 283 KTF GPQGGI+ D LAD I E +FP L +H ++ VAALAVA +E EYG Y R Sbjct: 181 GKTFSGPQGGIICWNTDRLADTIAETIFPVLTGSHQINRVAALAVAASEMLEYGPVYMRQ 240 Query: 284 TVRNAKALAEALYAEGLRVLCEHRGFTESHQIAVDVREQGGGAVIAEKLESANILCNKNL 343 V NA+ALAE L+ G+ VL RG+T++HQI VD R G G +LE+ANI+CN+ Sbjct: 241 VVANAQALAEFLHDRGINVLYAERGYTQTHQIVVDSRPAGSGRTAVRRLEAANIICNEMP 300 Query: 344 LPWDDESKSHDPSGIRLGTQELTRLGMGLSEMEYIAELIADVVLGRREPSEVRKDVEELR 403 LPWD +GIRLGT E+TR GMG++EME+IAE IA V+ G E + + +V + Sbjct: 301 LPWDSVETGGVETGIRLGTVEVTRRGMGVAEMEWIAERIAKVLHG-SEATAIAPEVADFL 359 Query: 404 REFQEVKY 411 F + Y Sbjct: 360 GRFDTIYY 367 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: 423 Number of extensions: 16 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: 376 Length adjustment: 31 Effective length of query: 397 Effective length of database: 345 Effective search space: 136965 Effective search space used: 136965 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: 50 (23.9 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