Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate WP_012332914.1 M446_RS14865 serine hydroxymethyltransferase
Query= metacyc::MONOMER-4244 (434 letters) >NCBI__GCF_000019365.1:WP_012332914.1 Length = 433 Score = 635 bits (1637), Expect = 0.0 Identities = 306/432 (70%), Positives = 361/432 (83%), Gaps = 3/432 (0%) Query: 6 AAGTAST---SRFFKSHVSETDPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAGSV 62 +AGTA T + FF + +++ DP++ A+Q+E GRQQHEIELIASENIVS+AVL+A GSV Sbjct: 2 SAGTAKTPLSNSFFSASLADVDPELSRAVQQELGRQQHEIELIASENIVSRAVLEAQGSV 61 Query: 63 LTNKYAEGYPGKRYYGGCQYVDIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNALA 122 LTNKYAEGYPG+RYYGGC++VDI E++AI+RAK+LF C+FANVQPNSGSQANQ VF A Sbjct: 62 LTNKYAEGYPGRRYYGGCEFVDIAENLAIERAKRLFGCDFANVQPNSGSQANQAVFMATM 121 Query: 123 QPGDTILGLSLAAGGHLTHGAPVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKPRI 182 QPGDT LGL LAAGGHLTHGAP N SGKWFK V Y V+ + IDM++V KLA+EHKP++ Sbjct: 122 QPGDTFLGLDLAAGGHLTHGAPPNVSGKWFKPVSYTVRREDQRIDMEQVAKLAEEHKPKV 181 Query: 183 IIAGGSAYPRKIDFAAFRAIADEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTTHK 242 IIAGGS YPR DFA FR IAD VGA+F VDMAHFAGLVA G+ PSPFPHAHVVTTTTHK Sbjct: 182 IIAGGSGYPRHWDFAKFREIADSVGAVFFVDMAHFAGLVAGGVHPSPFPHAHVVTTTTHK 241 Query: 243 TLRGPRGGMILTNDADIAKKINSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIKQV 302 TLRGPRGGM+LTND +AKKINSA+FPG+QGGPLMHVIAGKAVAFGEAL PDFK+Y KQV Sbjct: 242 TLRGPRGGMVLTNDEALAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALSPDFKIYAKQV 301 Query: 303 MDNARALGEVLVQNGFALVSGGTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGIPF 362 ++NA+AL + ++ GF + +GGTD HL+LVD+RPK LTG AE AL RA ITCNKNG+PF Sbjct: 302 VENAKALADTIISGGFDITTGGTDNHLMLVDMRPKNLTGKAAEAALSRAGITCNKNGVPF 361 Query: 363 DPEKPMVTSGIRLGSPAGTTRGFGVAEFQEIGRLISEVLDGVAKNGEDGNGAVEAAVKAK 422 DP+KP VTSGIRLG+PA T+RGFGVAEF+++G LI VLDG+A+ GE G+GA E V + Sbjct: 362 DPQKPTVTSGIRLGTPAATSRGFGVAEFKKVGELIVTVLDGLARAGEAGDGAAEKKVLEE 421 Query: 423 AIALCDRFPIYA 434 AL DRFPIYA Sbjct: 422 VHALTDRFPIYA 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: 643 Number of extensions: 26 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: 433 Length adjustment: 32 Effective length of query: 402 Effective length of database: 401 Effective search space: 161202 Effective search space used: 161202 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