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 WP_029131711.1 A3GO_RS0100345 serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >NCBI__GCF_000428045.1:WP_029131711.1 Length = 417 Score = 504 bits (1299), Expect = e-147 Identities = 253/405 (62%), Positives = 310/405 (76%), Gaps = 2/405 (0%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 D E++EAI E RQ H+ELIASEN+TS VM+AQGSV+TNKYAEG P KRYYGGCE+V Sbjct: 12 DDELWEAIQSEEVRQEEHIELIASENYTSPRVMQAQGSVLTNKYAEGYPGKRYYGGCEYV 71 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 DIAE LAI+RAKALF A++ANVQPHSG+QAN AVYMA+ +PGDT++GM L+HGGHLTHGA Sbjct: 72 DIAEQLAIDRAKALFGADYANVQPHSGSQANAAVYMALCQPGDTVLGMSLAHGGHLTHGA 131 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 K NFSGK+YNAV YG+ P T IDY ++ RLA EHKPK+IV G SAY RVIDW + R IA Sbjct: 132 KPNFSGKLYNAVQYGLDPATGEIDYAEVERLAGEHKPKMIVAGFSAYSRVIDWQRFRAIA 191 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCK--KEFAKD 245 D VGAY VDMAH AGLIA G+YP+PV A T+TTHKTLRGPR G IL K E K Sbjct: 192 DEVGAYFFVDMAHVAGLIAAGLYPSPVRIADVTTTTTHKTLRGPRGGLILAKANPELEKK 251 Query: 246 IDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVS 305 ++ VFPG QGGPLMHVIAAKAVAFKEAM FK Y +QV+ NA+ +A FI+ G+ VVS Sbjct: 252 LNSLVFPGTQGGPLMHVIAAKAVAFKEAMEPGFKTYQQQVMTNAQAMASVFIERGYDVVS 311 Query: 306 GGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMTT 365 GGT+ H+ L+ GLTG++V+ LG ANITVN NAVP DP P TSGIR+GTPA+TT Sbjct: 312 GGTNDHLFLVSFIQAGLTGKDVDAWLGAANITVNMNAVPNDPQSPFITSGIRVGTPALTT 371 Query: 366 RGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 RG+ E + + +A + VI + GD+ I+ V+ +V+++C++ P+Y Sbjct: 372 RGVGEAEAKELAGWMCDVIDSRGDQTAIDRVKVQVLDLCKRHPVY 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: 594 Number of extensions: 23 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 Sep 24 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