Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_010527895.1 GQW_RS0110425 serine hydroxymethyltransferase
Query= BRENDA::Q5SI56 (407 letters) >NCBI__GCF_000220155.1:WP_010527895.1 Length = 426 Score = 476 bits (1225), Expect = e-139 Identities = 237/412 (57%), Positives = 300/412 (72%), Gaps = 17/412 (4%) Query: 5 LKRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGYPGARYYGGC 64 +KRDE +F LI E++RQ G+ELIASENFVS QV A+GS +TNKYAEG PG RYYGGC Sbjct: 1 MKRDEKIFALIEKEKQRQLNGIELIASENFVSDQVMAAMGSCMTNKYAEGLPGKRYYGGC 60 Query: 65 EVIDRVESLAIERAKALFGAAWANVQPHSGSQANMAVYMALMEPGDTLMGMDLAAGGHLT 124 +V+D E+LAIER K LF A WANVQPHSG+QANMAV M ++ PGD +G+DLA GGHL+ Sbjct: 61 QVVDESETLAIERLKELFDAEWANVQPHSGAQANMAVLMTVLNPGDKFLGLDLAHGGHLS 120 Query: 125 HGSRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGASAYPRFWDFKAFR 184 HGS VN SGKLY+ ++YGV+ DT L+D + + +LALEH+PK+I+ GASAY R WD++ R Sbjct: 121 HGSPVNSSGKLYQPIAYGVKEDTGLVDYDMMEQLALEHKPKLIIGGASAYSRDWDYERMR 180 Query: 185 EIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGPRGGLILSNDP--- 241 IAD+VGA L++DMAH AGL+AAGL NP+ YAH+VTSTTHKTLRGPRGG+IL Sbjct: 181 AIADKVGAILMIDMAHPAGLIAAGLLKNPVKYAHIVTSTTHKTLRGPRGGIILMGKDFDN 240 Query: 242 ------------ELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVEN 289 ++ +D +FPGIQGGPLEH+IA KAVAF+EALQPE+KEY + V +N Sbjct: 241 PMGIKTKKGEIRKMSSLLDSAVFPGIQGGPLEHIIAAKAVAFYEALQPEYKEYQKQVQKN 300 Query: 290 AKRLAEELARRGYRIVTGGTDNHLFLVDLRPK--GLTGKEAEERLDAVGITVNKNAIPFD 347 A+++AE +GY++++GGTDNH L+DLR K LTGK+AE L IT+NKN +PFD Sbjct: 301 ARKMAECFMAKGYKVISGGTDNHSMLIDLRTKFPELTGKKAENTLVLADITINKNMVPFD 360 Query: 348 PKPPRVTSGIRIGTPAITTRGFTPEEMPLVAELIDRALLEGPSEALREEVRR 399 + P TSGIR+GT A+TTRG E M V + ID L SE V++ Sbjct: 361 DRSPFQTSGIRVGTAALTTRGLKEEHMISVVDFIDEVLSNPDSEETITSVQK 412 Lambda K H 0.319 0.137 0.398 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: 532 Number of extensions: 19 Number of successful extensions: 4 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: 407 Length of database: 426 Length adjustment: 31 Effective length of query: 376 Effective length of database: 395 Effective search space: 148520 Effective search space used: 148520 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