Align Serine hydroxymethyltransferase; SHMT; Serine methylase; L-threonine/L-allo-threonine aldolase; EC 2.1.2.1; EC 4.1.2.48 (characterized)
to candidate Synpcc7942_0282 Synpcc7942_0282 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >FitnessBrowser__SynE:Synpcc7942_0282 Length = 427 Score = 508 bits (1309), Expect = e-148 Identities = 253/407 (62%), Positives = 308/407 (75%), Gaps = 1/407 (0%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 D I I +E +RQ HLELIASENF S AVM AQGSV+TNKYAEGLP KRYYGGCEFV Sbjct: 13 DPAIAAIIGRELQRQQEHLELIASENFASPAVMAAQGSVLTNKYAEGLPSKRYYGGCEFV 72 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 D AE+LAIERAK LF A HANVQPHSG QAN AV++ +L+PGDT +GMDLSHGGHLTHG+ Sbjct: 73 DQAEELAIERAKELFGAAHANVQPHSGAQANFAVFLTLLQPGDTFLGMDLSHGGHLTHGS 132 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 VN SGK +NA +YGV+ ET +DYD + LA +H+PKLI+ G SAYPR ID+AK REIA Sbjct: 133 PVNVSGKWFNAGHYGVNRETERLDYDAIRELALQHRPKLIICGYSAYPRTIDFAKFREIA 192 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCK-KEFAKDI 246 D VGAYL+ DMAH AGL+A G++P+P+P+ VT+TTHKTLRGPR G IL + E K + Sbjct: 193 DEVGAYLLADMAHIAGLVAAGLHPSPIPHCDVVTTTTHKTLRGPRGGLILTRDAELGKKL 252 Query: 247 DKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVSG 306 DKSVFPG QGGPL HVIAAKAVAF EA+ EFK Y+ QV+ANA+ LA + G K+VS Sbjct: 253 DKSVFPGTQGGPLEHVIAAKAVAFGEALRPEFKTYSAQVIANAQALARQLQARGLKIVSD 312 Query: 307 GTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMTTR 366 GTD+H++L+DLR G+TG+ + + NIT NKN VPFDP P TSGIRLGT AMTTR Sbjct: 313 GTDNHLLLVDLRSIGMTGKVADLLVSDVNITANKNTVPFDPESPFVTSGIRLGTAAMTTR 372 Query: 367 GMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLYPEL 413 G KE + I+A +I+ + N D + + R+ V+E+C++FPLYP L Sbjct: 373 GFKEAEFAIVADIIADRLLNPEDSSMEDSCRRRVLELCQRFPLYPHL 419 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: 598 Number of extensions: 24 Number of successful extensions: 2 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: 427 Length adjustment: 32 Effective length of query: 395 Effective length of database: 395 Effective search space: 156025 Effective search space used: 156025 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 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