Align Serine hydroxymethyltransferase 2; SHMT 2; Serine methylase 2; EC 2.1.2.1 (characterized)
to candidate WP_010441641.1 G7G_RS0111845 serine hydroxymethyltransferase
Query= SwissProt::Q3JGP5 (424 letters) >NCBI__GCF_000192475.1:WP_010441641.1 Length = 417 Score = 583 bits (1504), Expect = e-171 Identities = 288/417 (69%), Positives = 341/417 (81%), Gaps = 1/417 (0%) Query: 8 FSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGKR 67 F +SL E D + +I +E +RQ Q+ELIASENIVS+AV+DAQGSVLTNKYAEGYPG+R Sbjct: 2 FKKSLIEADPVIASSIAREGKRQAEQIELIASENIVSQAVIDAQGSVLTNKYAEGYPGRR 61 Query: 68 YYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSLDA 127 YYGGCE+ DEVEA AIER+K+LF +ANVQPHSGAQANGAV LAL PGDT+LGMSLDA Sbjct: 62 YYGGCEYVDEVEAEAIERLKQLFGCEYANVQPHSGAQANGAVKLALLSPGDTILGMSLDA 121 Query: 128 GGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLD 187 GGHLTHGAKPA SGKWF +QYG++ + LIDYDQVEALA+ KP LIIAG SAY +K+D Sbjct: 122 GGHLTHGAKPAQSGKWFRPVQYGLT-EAGLIDYDQVEALAKAEKPQLIIAGASAYSQKID 180 Query: 188 FARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTN 247 FARFRAIAD VGA L+ DMAHIAG++A G H +PV HAHV+TSTTHKTLRGPRGG +LTN Sbjct: 181 FARFRAIADEVGAWLLADMAHIAGLVATGLHPSPVGHAHVITSTTHKTLRGPRGGVILTN 240 Query: 248 DEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKA 307 DE +AKK+NSAVFPGLQGGPLMHVIAGKAVAFGEAL +FK Y+ RV+ +A AL +V+ A Sbjct: 241 DEALAKKMNSAVFPGLQGGPLMHVIAGKAVAFGEALKPEFKEYMKRVVVSASALANVMIA 300 Query: 308 GGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRL 367 G D+V+GGT+NHL+LVDLRP G+ G E ALERAG TCNKN +P DP+KPTITSGIRL Sbjct: 301 RGCDIVSGGTENHLMLVDLRPIGVTGKDAEAALERAGFTCNKNSVPGDPQKPTITSGIRL 360 Query: 368 GTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424 GT AG +RGFG+ EF+++G LI V +AL +P+GD A E+ R ++ ALC PIY Sbjct: 361 GTAAGCSRGFGSEEFKQIGHLIGNVLDALAQSPDGDEAVEKETREKVRALCASHPIY 417 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: 639 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: 424 Length of database: 417 Length adjustment: 32 Effective length of query: 392 Effective length of database: 385 Effective search space: 150920 Effective search space used: 150920 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: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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