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 PfGW456L13_1116 Serine hydroxymethyltransferase (EC 2.1.2.1)
Query= SwissProt::D3DKC4 (427 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1116 Length = 417 Score = 492 bits (1266), Expect = e-143 Identities = 247/405 (60%), Positives = 304/405 (75%), Gaps = 2/405 (0%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 D + A+ E +RQ H+ELIASEN+TS VMEAQGS +TNKYAEG P KRYYGGCE V Sbjct: 12 DDALLAAMNAEEQRQEDHIELIASENYTSKRVMEAQGSGLTNKYAEGYPGKRYYGGCEHV 71 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 D E LAIERAK LF A++ANVQPHSG+ AN AVY+A+L+ GDTI+GM L+HGGHLTHGA Sbjct: 72 DKVEALAIERAKQLFGADYANVQPHSGSSANSAVYLALLQAGDTILGMSLAHGGHLTHGA 131 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 KV+ SGK+YNAV YG+ T LIDYD++ RLA EHKPK+IV G SAY + +D+ + R+IA Sbjct: 132 KVSSSGKLYNAVQYGIDTNTGLIDYDEVERLAVEHKPKMIVAGFSAYSKTLDFPRFRQIA 191 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCK--KEFAKD 245 D VGA L VDMAH AGL+A G+YPNP+PYA VT+TTHKTLRGPR G IL K +E K Sbjct: 192 DKVGALLFVDMAHVAGLVAAGLYPNPLPYADVVTTTTHKTLRGPRGGLILAKSNEEIEKK 251 Query: 246 IDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVS 305 ++ +VFPG QGGPLMHVIA KAV FKEA+ FK Y +QV+ NA+ +A FIK G+ VVS Sbjct: 252 LNAAVFPGAQGGPLMHVIAGKAVCFKEALEPGFKAYQQQVIDNAQAMAGVFIKRGYDVVS 311 Query: 306 GGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMTT 365 GGTD+H+ L+ L GLTG+E + ALG+A+ITVNKNAVP DP P TSG+R+GTPA+TT Sbjct: 312 GGTDNHLFLVSLIRQGLTGKEADAALGRAHITVNKNAVPNDPQSPFVTSGLRIGTPAVTT 371 Query: 366 RGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 RG K Q +A I ++ N+GD V V ++V +C FP+Y Sbjct: 372 RGFKVTQCVTLAGWICDILDNLGDADVEANVAEQVAALCADFPVY 416 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: 575 Number of extensions: 28 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: 417 Length adjustment: 32 Effective length of query: 395 Effective length of database: 385 Effective search space: 152075 Effective search space used: 152075 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: 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