Align Serine hydroxymethyltransferase 2; SHMT 2; Serine methylase 2; EC 2.1.2.1 (characterized)
to candidate WP_028310558.1 H566_RS0104925 serine hydroxymethyltransferase
Query= SwissProt::Q3JGP5 (424 letters) >NCBI__GCF_000482785.1:WP_028310558.1 Length = 425 Score = 648 bits (1672), Expect = 0.0 Identities = 319/423 (75%), Positives = 363/423 (85%) Query: 2 SNANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAE 61 S+ + FF S+A D ++R + EL RQQ +ELIASENIVSRAVL+AQGSVLTNKYAE Sbjct: 3 SHLHAFFHASVAASDPAIRDGLDAELVRQQEGIELIASENIVSRAVLEAQGSVLTNKYAE 62 Query: 62 GYPGKRYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVL 121 GYPGKRYYGGCE DEVEALAIER+ +LF A +ANVQPHSGA AN AVMLA+AKPGDT+L Sbjct: 63 GYPGKRYYGGCECVDEVEALAIERICKLFGAQYANVQPHSGASANTAVMLAIAKPGDTIL 122 Query: 122 GMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSA 181 GMSLDAGGHLTHGAKPALSGKWFNA+QYGV R+ +D +QVE LA +HKPS+IIAG+SA Sbjct: 123 GMSLDAGGHLTHGAKPALSGKWFNAVQYGVRREDQRLDLEQVEKLAHEHKPSVIIAGYSA 182 Query: 182 YPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRG 241 YPR +DF+ FR IAD VGA LMVDMAH AG++AAGRH NP++HAH+VT+TTHKTLRGPRG Sbjct: 183 YPRAIDFSAFRKIADDVGATLMVDMAHFAGIVAAGRHQNPLDHAHIVTTTTHKTLRGPRG 242 Query: 242 GFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQAL 301 G +LTNDE +AKKINSAVFPG QGGPLMHVIA KAVAFGEAL +F++YID+VLANA+ L Sbjct: 243 GAILTNDEALAKKINSAVFPGAQGGPLMHVIAAKAVAFGEALRPEFRSYIDQVLANARVL 302 Query: 302 GDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTI 361 G+VL AGGVDLVTGGTDNHLLLVDLRPKGLKG QV+ AL RAGITCNKNGIPFDPEKP + Sbjct: 303 GEVLTAGGVDLVTGGTDNHLLLVDLRPKGLKGNQVDAALGRAGITCNKNGIPFDPEKPMV 362 Query: 362 TSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERF 421 TSGIRLGTPA TTRGFG AEFR+VG LIL+VF++L PEGD E VR E+ ALCE+F Sbjct: 363 TSGIRLGTPACTTRGFGEAEFRKVGELILKVFDSLAAKPEGDAEVEAAVRAEVKALCEQF 422 Query: 422 PIY 424 PIY Sbjct: 423 PIY 425 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: 696 Number of extensions: 27 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: 425 Length adjustment: 32 Effective length of query: 392 Effective length of database: 393 Effective search space: 154056 Effective search space used: 154056 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