Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate WP_012044666.1 BBTA_RS21765 serine hydroxymethyltransferase
Query= metacyc::MONOMER-4244 (434 letters) >NCBI__GCF_000015165.1:WP_012044666.1 Length = 434 Score = 608 bits (1567), Expect = e-178 Identities = 301/433 (69%), Positives = 348/433 (80%) Query: 1 MSSAPAAGTASTSRFFKSHVSETDPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAG 60 M+++ A +S FF + ++E DP+I +AI+ E GRQ+HEIELIASENIVS+AVL+A G Sbjct: 1 MTASSAKPASSVDSFFSATLAEADPEIAAAIKGELGRQRHEIELIASENIVSRAVLEAQG 60 Query: 61 SVLTNKYAEGYPGKRYYGGCQYVDIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNA 120 SV+TNKYAEGYPG RYYGGC++VD+ E++AIDRAKKLF FANVQPNSGSQ NQ VF A Sbjct: 61 SVMTNKYAEGYPGARYYGGCEWVDVAENLAIDRAKKLFGANFANVQPNSGSQMNQAVFLA 120 Query: 121 LAQPGDTILGLSLAAGGHLTHGAPVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKP 180 L QPGDT +GL LAAGGHLTHG+PVN SGKWFKA HY V+ D HLIDMD V K A+E KP Sbjct: 121 LLQPGDTFMGLDLAAGGHLTHGSPVNMSGKWFKAAHYTVRRDDHLIDMDAVAKQAEEVKP 180 Query: 181 RIIIAGGSAYPRKIDFAAFRAIADEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTT 240 ++IIAGGSAY R DF FR IAD VGA LVDMAHFAGLVA G SP PHAH+VTTTT Sbjct: 181 KLIIAGGSAYSRPWDFKRFREIADHVGAYLLVDMAHFAGLVAGGAHASPVPHAHIVTTTT 240 Query: 241 HKTLRGPRGGMILTNDADIAKKINSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIK 300 HK+LRGPRGG+IL ND KK+NSAIFPG+QGGPLMHVIA KAVAF EALRP+FK Y K Sbjct: 241 HKSLRGPRGGLILWNDEQFTKKLNSAIFPGLQGGPLMHVIAAKAVAFAEALRPEFKTYAK 300 Query: 301 QVMDNARALGEVLVQNGFALVSGGTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGI 360 +++NA+AL E L GF +VSGGTD HL+LVDLRPK L G +EKAL RA ITCNKNGI Sbjct: 301 NIVENAKALAESLRAQGFDIVSGGTDNHLMLVDLRPKGLKGNVSEKALVRAGITCNKNGI 360 Query: 361 PFDPEKPMVTSGIRLGSPAGTTRGFGVAEFQEIGRLISEVLDGVAKNGEDGNGAVEAAVK 420 PFDPEKP VTSG+RLG+PA TTRGFGVAEFQ++G LI+EVL+ +A+ + VEAAVK Sbjct: 361 PFDPEKPFVTSGLRLGTPAATTRGFGVAEFQQVGSLIAEVLNAIAQAPDGSAPLVEAAVK 420 Query: 421 AKAIALCDRFPIY 433 AK AL DRFPIY Sbjct: 421 AKVKALTDRFPIY 433 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: 599 Number of extensions: 15 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: 434 Length of database: 434 Length adjustment: 32 Effective length of query: 402 Effective length of database: 402 Effective search space: 161604 Effective search space used: 161604 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