Align Serine hydroxymethyltransferase 2; SHMT 2; Serine methylase 2; EC 2.1.2.1 (characterized)
to candidate WP_013091662.1 BC1002_RS19295 serine hydroxymethyltransferase
Query= SwissProt::Q3JGP5 (424 letters) >NCBI__GCF_000092885.1:WP_013091662.1 Length = 424 Score = 751 bits (1940), Expect = 0.0 Identities = 376/424 (88%), Positives = 395/424 (93%) Query: 1 MSNANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYA 60 MSN NPFF SL RD +VRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYA Sbjct: 1 MSNPNPFFEDSLPARDPAVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYA 60 Query: 61 EGYPGKRYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTV 120 EGYPGKRYYGGCE+ DE+E LA++R+K+LFNA ANVQPHSGAQANGAVMLAL KPGDTV Sbjct: 61 EGYPGKRYYGGCEYVDEIETLALDRIKQLFNAKFANVQPHSGAQANGAVMLALTKPGDTV 120 Query: 121 LGMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFS 180 LGMSLDAGGHLTHGAKPALSGKWFNA+QYGV DTMLIDY+Q+E LAQQHKP+L+IAGFS Sbjct: 121 LGMSLDAGGHLTHGAKPALSGKWFNAVQYGVRCDTMLIDYEQIEELAQQHKPTLLIAGFS 180 Query: 181 AYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPR 240 AYPR LDFAR RAIAD VGAKLMVDMAHIAGVIAAGRH NPV HAHVVTSTTHKTLRGPR Sbjct: 181 AYPRALDFARLRAIADGVGAKLMVDMAHIAGVIAAGRHDNPVPHAHVVTSTTHKTLRGPR 240 Query: 241 GGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQA 300 GGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEAL FKTYID VLANA+A Sbjct: 241 GGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALQPGFKTYIDSVLANARA 300 Query: 301 LGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPT 360 LGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKG QVEQALERAGITCNKNGIPFD EKPT Sbjct: 301 LGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGNQVEQALERAGITCNKNGIPFDTEKPT 360 Query: 361 ITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCER 420 +TSGIRLGTPAGTTRGFG +EFREVGRLI+EV +ALRT+ EGD ATEQRVRREIFALC+R Sbjct: 361 VTSGIRLGTPAGTTRGFGVSEFREVGRLIVEVLDALRTSAEGDAATEQRVRREIFALCDR 420 Query: 421 FPIY 424 FPIY Sbjct: 421 FPIY 424 Lambda K H 0.318 0.136 0.391 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: 731 Number of extensions: 21 Number of successful extensions: 1 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: 424 Length of database: 424 Length adjustment: 32 Effective length of query: 392 Effective length of database: 392 Effective search space: 153664 Effective search space used: 153664 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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