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 WP_013705554.1 DESAC_RS02750 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_000195295.1:WP_013705554.1 Length = 429 Score = 485 bits (1248), Expect = e-141 Identities = 238/420 (56%), Positives = 312/420 (74%), Gaps = 10/420 (2%) Query: 1 MRHLFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRY 60 M L D EIY AI +E +RQ LELIASENF S AV+EAQGS++T+KYAEG P +RY Sbjct: 1 MSSLAQIDPEIYAAIQQEEQRQLTKLELIASENFVSPAVLEAQGSILTHKYAEGYPGRRY 60 Query: 61 YGGCEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHG 120 YGGCE VD AE LAI RAK LF E+ NVQPHSGTQANMA+Y A LKPGD I+GMDL+HG Sbjct: 61 YGGCEHVDTAETLAINRAKQLFGVEYVNVQPHSGTQANMAIYFAFLKPGDAILGMDLAHG 120 Query: 121 GHLTHGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDW 180 GHL+HGA VNFSG++Y ++ YGV ++ ID++ + K+H+P+++V GASAYPR +D+ Sbjct: 121 GHLSHGAAVNFSGQLYRSLSYGVKKDSGEIDFEGIEACLKKHRPRMLVAGASAYPRTLDF 180 Query: 181 AKLREIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILC-- 238 + ++A GA LMVD+AH AGL+A G++P+P P A F+TSTTHKTLRGPR G IL Sbjct: 181 ERFAQLARHYGALLMVDIAHIAGLVAAGLHPSPTPSADFITSTTHKTLRGPRGGLILAQN 240 Query: 239 -------KKEF-AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANAR 290 K+EF A+ +D +FPGIQGGPLMH IAAKAVAF+EA+ FK Y +Q++ NAR Sbjct: 241 REIELQGKQEFYAQRLDFYLFPGIQGGPLMHTIAAKAVAFQEALRPAFKRYQQQILLNAR 300 Query: 291 VLAEEFIKEGFKVVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPP 350 +AEEF++ G+K+V+GGTD+H++L+DL TGLTG++ E AL +A ITVNKN +PFDP P Sbjct: 301 TMAEEFLQRGYKLVTGGTDNHLLLIDLSKTGLTGQQAEIALDQAGITVNKNRIPFDPRPA 360 Query: 351 VKTSGIRLGTPAMTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 TSGIR+GTPA+TTRGMK +MR + I + + D +E++++EV + C +PL+ Sbjct: 361 KVTSGIRIGTPALTTRGMKAPEMRQVVDFIHRALSAPTDVSSLEHLQKEVKDFCRTYPLF 420 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: 604 Number of extensions: 25 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: 429 Length adjustment: 32 Effective length of query: 395 Effective length of database: 397 Effective search space: 156815 Effective search space used: 156815 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