Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate WP_012335076.1 M446_RS25920 serine hydroxymethyltransferase
Query= metacyc::MONOMER-4244 (434 letters) >NCBI__GCF_000019365.1:WP_012335076.1 Length = 422 Score = 441 bits (1135), Expect = e-128 Identities = 227/412 (55%), Positives = 283/412 (68%), Gaps = 6/412 (1%) Query: 22 ETDPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAGSVLTNKYAEGYPGKRYYGGCQ 81 + DPD+ +AI+ E RQQ IELIASENIVS+ VL+A GSVLTNK EG P RYYGG Sbjct: 14 DADPDLAAAIRGELARQQAGIELIASENIVSRLVLEAQGSVLTNKTVEGLPFARYYGGAD 73 Query: 82 YVDIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNALAQPGDTILGLSLAAGGHLTH 141 + D +ED+AI RA +LF C FANVQP+SGS AN GVF L GDTIL + AAGGH++H Sbjct: 74 FADAIEDLAIRRAARLFGCRFANVQPHSGSNANAGVFLGLIALGDTILAMDTAAGGHISH 133 Query: 142 GAPVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKPRIIIAGGSAYPRKIDFAAFRA 201 G P +G+ ++ + Y V S +D+D VR LA+ H+PR+I+AGGSAYP +DFA FRA Sbjct: 134 GHPATLTGRDYRILRYGVDRASECVDLDAVRALARAHRPRMIVAGGSAYPGALDFAGFRA 193 Query: 202 IADEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTTHKTLRGPRGGMILTNDADIAK 261 +ADEVGA+ +VDMAH AGLVA GL P PFPHAHVVT+TT+K+LRG RGG +L ND + Sbjct: 194 VADEVGALLMVDMAHVAGLVATGLYPHPFPHAHVVTSTTYKSLRGARGGFVLWNDPALGD 253 Query: 262 KINSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIKQVMDNARALGEVLVQNGFALV 321 +I S IFPG+QG ++H +AGKA FGEALRP+F+ Y + V+DNA+AL L G LV Sbjct: 254 RIQSGIFPGVQGSVMLHAVAGKAACFGEALRPEFRAYNQAVLDNAQALAAGLAAQGLRLV 313 Query: 322 SGGTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGIPFDPEKPMVTSGIRLGSPAGT 381 SGGT + L+LVDL TG A KAL RA + NKN IP+DP P SG+RL + AGT Sbjct: 314 SGGTASGLMLVDLTGTGTTGDVAAKALERAGLAVNKNLIPYDPRPPEAPSGLRLSANAGT 373 Query: 382 TRGFGVAEFQEIGRLISEVLDGVAKNGEDGNGAVEAAVKAKAIALCDRFPIY 433 TRGFG AEF I I ++ A + + V+A+ ALC FPIY Sbjct: 374 TRGFGRAEFAVIAGWIGRIVRAPA------DADLAGRVRAEVEALCRAFPIY 419 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: 572 Number of extensions: 23 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: 422 Length adjustment: 32 Effective length of query: 402 Effective length of database: 390 Effective search space: 156780 Effective search space used: 156780 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