Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1; L-threonine/L-allo-threonine aldolase; EC 4.1.2.48 (uncharacterized)
to candidate Dsui_2254 Dsui_2254 glycine/serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__PS:Dsui_2254 Length = 433 Score = 450 bits (1157), Expect = e-131 Identities = 229/409 (55%), Positives = 291/409 (71%), Gaps = 7/409 (1%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 D E + EY RQ + +ELIASEN S AV+E QGSV+TNKYAEG P +RYYGGC V Sbjct: 23 DPEAARYVAAEYARQRHSIELIASENIVSRAVLEMQGSVLTNKYAEGYPGRRYYGGCGPV 82 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 D E LAI RAK LF +ANVQPHSG+QAN AVY+A+L+PGDTI+G+ L+ GGHLTHGA Sbjct: 83 DGVEALAIARAKGLFGCAYANVQPHSGSQANQAVYLALLQPGDTILGLGLAAGGHLTHGA 142 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 +N SGK + V YGV + H ID Q+ +LA E++PKLI+ G SAY R++D+A+ R IA Sbjct: 143 PMNQSGKWFRGVAYGVRADDHRIDMAQVEQLAYEYRPKLIIAGGSAYSRILDFAEFRRIA 202 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCK-KEFAKDI 246 D VGA L+VDMAH+AGL+AGG +P+P+PYA VTSTTHKTLRGPR G IL K I Sbjct: 203 DRVGARLLVDMAHFAGLVAGGAHPSPLPYADVVTSTTHKTLRGPRGGLILSNDAALGKAI 262 Query: 247 DKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVSG 306 D +VFPG+QGGPLMHVI AKAVAF EA+ EF+ YA +VV NA+ LA+ G ++VSG Sbjct: 263 DSAVFPGLQGGPLMHVIGAKAVAFGEALQPEFRSYAARVVENAQALADALAAGGLRIVSG 322 Query: 307 GTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMTTR 366 GTD+H+ + DLR LTG E+AL + IT+NKNA+P DP P+ TSGIR+G+PA T+R Sbjct: 323 GTDTHLAVADLRPLNLTGNVAEKALERVGITLNKNAIPHDPQKPMVTSGIRVGSPAGTSR 382 Query: 367 GMKEDQMRIIARLISKVIKNIG------DEKVIEYVRQEVIEMCEQFPL 409 G + + R+I LI +++ + D V VR +V E+C +FPL Sbjct: 383 GFRTAEFRLIGGLIVHLLEALAANPEAPDPAVAAAVRAQVAELCRRFPL 431 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: 603 Number of extensions: 24 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: 433 Length adjustment: 32 Effective length of query: 395 Effective length of database: 401 Effective search space: 158395 Effective search space used: 158395 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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