Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate WP_011424840.1 RHE_RS07695 serine hydroxymethyltransferase
Query= metacyc::MONOMER-4244 (434 letters) >NCBI__GCF_000092045.1:WP_011424840.1 Length = 432 Score = 607 bits (1566), Expect = e-178 Identities = 296/425 (69%), Positives = 345/425 (81%), Gaps = 1/425 (0%) Query: 10 ASTSRFFKSHVSETDPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAGSVLTNKYAE 69 AST FF +++ DP+IF AI KE GRQ+HEIELIASENIVS+AVL+A GS++TNKYAE Sbjct: 4 ASTESFFNRSLADVDPEIFGAIGKELGRQRHEIELIASENIVSRAVLEAQGSIMTNKYAE 63 Query: 70 GYPGKRYYGGCQYVDIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNALAQPGDTIL 129 GYPGKRYYGGCQ+VDI E++AI+RAKKLF FANVQPNSGSQ NQ VF AL QPGDT + Sbjct: 64 GYPGKRYYGGCQFVDIAEELAIERAKKLFGVNFANVQPNSGSQMNQAVFLALLQPGDTFM 123 Query: 130 GLSLAAGGHLTHGAPVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKPRIIIAGGSA 189 GL L +GGHLTHG+PVN SGKWF V Y V+ +L+DMDEV + A+EHKP++IIAGG+A Sbjct: 124 GLDLNSGGHLTHGSPVNMSGKWFNVVSYGVREGDNLLDMDEVARKAEEHKPKVIIAGGTA 183 Query: 190 YPRKIDFAAFRAIADEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTTHKTLRGPRG 249 Y R D+ FR IAD VGA +VDMAH AGLVA G PSPFPH HV TTTTHK+LRGPRG Sbjct: 184 YSRIWDWKRFREIADSVGAYLMVDMAHIAGLVAGGQHPSPFPHCHVATTTTHKSLRGPRG 243 Query: 250 GMILTNDADIAKKINSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIKQVMDNARAL 309 G+ILTN+ D+AKK NSA+FPG+QGGPLMH+IA KAVAFGEAL+P+FK Y Q++ NARAL Sbjct: 244 GVILTNEEDLAKKFNSAVFPGLQGGPLMHIIAAKAVAFGEALQPEFKEYAAQIVKNARAL 303 Query: 310 GEVLVQNGFALVSGGTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGIPFDPEKPMV 369 E L+ G +VSGGTD HL+LVDLR K TG +AE ALGRA ITCNKNGIPFDPEKP V Sbjct: 304 AETLIAGGLDVVSGGTDNHLMLVDLRKKNATGKRAEAALGRAYITCNKNGIPFDPEKPFV 363 Query: 370 TSGIRLGSPAGTTRGFGVAEFQEIGRLISEVLDGV-AKNGEDGNGAVEAAVKAKAIALCD 428 TSG+RLG+PAGTTRGF AEF+EIG LI EVLDG+ N +DGN AVEAAV+ K + L D Sbjct: 364 TSGVRLGAPAGTTRGFKEAEFREIGNLIVEVLDGLKVANSDDGNAAVEAAVRGKVVNLTD 423 Query: 429 RFPIY 433 RFP+Y Sbjct: 424 RFPMY 428 Lambda K H 0.319 0.136 0.396 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: 609 Number of extensions: 20 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: 434 Length of database: 432 Length adjustment: 32 Effective length of query: 402 Effective length of database: 400 Effective search space: 160800 Effective search space used: 160800 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