Align Serine hydroxymethyltransferase 2; SHMT 2; Serine methylase 2; EC 2.1.2.1 (characterized)
to candidate H281DRAFT_02468 H281DRAFT_02468 serine hydroxymethyltransferase
Query= SwissProt::Q3JGP5 (424 letters) >FitnessBrowser__Burk376:H281DRAFT_02468 Length = 424 Score = 756 bits (1953), Expect = 0.0 Identities = 376/424 (88%), Positives = 399/424 (94%) Query: 1 MSNANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYA 60 MSN NPFF +SLA RD +VRGAILKELERQQSQVELIASENIVSRAVL+AQGSVLTNKYA Sbjct: 1 MSNPNPFFEESLATRDQAVRGAILKELERQQSQVELIASENIVSRAVLEAQGSVLTNKYA 60 Query: 61 EGYPGKRYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTV 120 EGYPGKRYYGGCE+ DE+E LA+ER+K+LFNA ANVQPHSGAQANGAVMLAL KPGDTV Sbjct: 61 EGYPGKRYYGGCEYVDEIETLALERIKQLFNAKFANVQPHSGAQANGAVMLALVKPGDTV 120 Query: 121 LGMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFS 180 LGMSLDAGGHLTHGAKPA+SGKWFNA+QYGV+RDT+LIDYDQ+E LAQQHKP+L+IAGFS Sbjct: 121 LGMSLDAGGHLTHGAKPAMSGKWFNAVQYGVNRDTLLIDYDQIEELAQQHKPALLIAGFS 180 Query: 181 AYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPR 240 AYPR LDF R RAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPR Sbjct: 181 AYPRALDFKRLRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPR 240 Query: 241 GGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQA 300 GGFVLTNDE+IAKKINSAVFPGLQGGPLMHVIAGKAVAFGEAL FKTYID VLANAQA Sbjct: 241 GGFVLTNDEDIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALQPGFKTYIDNVLANAQA 300 Query: 301 LGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPT 360 LG+VLKAGGVDLVTGGTDNHLLLVDLRPKGLKG QVEQALERAGITCNKNGIPFD EKPT Sbjct: 301 LGEVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGNQVEQALERAGITCNKNGIPFDTEKPT 360 Query: 361 ITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCER 420 ITSG+RLGTPAGTTRGFG EFR+VGRLI+EV ++LR +PEG ATEQRVRREIFALCER Sbjct: 361 ITSGVRLGTPAGTTRGFGVNEFRDVGRLIVEVLDSLRDHPEGHAATEQRVRREIFALCER 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: 751 Number of extensions: 20 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 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