Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_015799196.1 AFER_RS09320 serine hydroxymethyltransferase
Query= BRENDA::Q5SI56 (407 letters) >NCBI__GCF_000023265.1:WP_015799196.1 Length = 424 Score = 442 bits (1137), Expect = e-129 Identities = 239/416 (57%), Positives = 289/416 (69%), Gaps = 15/416 (3%) Query: 6 KRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGYPGARYYGGCE 65 K D L L+ E++RQR L+LIASENF S V EA GSVLTNKYAEGYPG RYYGG Sbjct: 6 KEDPELAALLVREQERQRSTLQLIASENFTSAAVLEATGSVLTNKYAEGYPGRRYYGGNA 65 Query: 66 VIDRVESLAIERAKALFGAAWANVQPHSGSQANMAVYMALMEPGDTLMGMDLAAGGHLTH 125 V+D VESLAIERA+ALF A WANVQPH+G+ AN A Y+AL+ PGD ++ M L GGHLTH Sbjct: 66 VVDEVESLAIERARALFRAPWANVQPHAGANANAAAYLALLAPGDPVLAMRLDQGGHLTH 125 Query: 126 GSRVNFSGKLYKVVSYGVR---PDTELIDLEEVRRLALEHRPKVIVAGASAYPRFWDFKA 182 GS VNFSG+LY+ V YGVR P+ E +DL+++ LA H P++IV GA+AYPR D Sbjct: 126 GSPVNFSGQLYRFVGYGVRQEDPNREWLDLDQLADLARAHHPRLIVVGATAYPRVIDVTP 185 Query: 183 FREIADEVGAYLVVDMAHFAGLVAAGLHPNPL------PYAHVVTSTTHKTLRGPRGGLI 236 R IADEVGA ++ D AH AGL+AAG++PNPL A VVT TTHKTLRGPRG I Sbjct: 186 IRAIADEVGARVLFDAAHVAGLIAAGVYPNPLWLASGERGADVVTFTTHKTLRGPRGAAI 245 Query: 237 LSNDPELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVENAKRLAEE 296 + ++ ++ K IDK +FPG+QGGPLEH IA KAVAF EA P F++Y R VV NA+ LA Sbjct: 246 VGHE-DVAKAIDKAVFPGLQGGPLEHAIAAKAVAFREAASPSFRDYGRRVVANAQTLAAS 304 Query: 297 LARRGYRIVTGGTDNHLFLVDLR--PKGLTGKEAEERLDAVGITVNKNAIPFDPKPPRVT 354 L G+R+V+GGTD HL LVDLR L GK A++ LDA GIT+N+N IPFDP+ P VT Sbjct: 305 LEAEGFRLVSGGTDVHLILVDLRDFDPELDGKTAQDLLDAAGITLNRNQIPFDPRSPFVT 364 Query: 355 SGIRIGTPAITTRGFTPEEMPLVAELIDRALLEGPSEALRE---EVRRLALAHPMP 407 SG+R+GT A+TT G EEM V LI L E +RE +VR L A P Sbjct: 365 SGLRLGTAALTTTGMGEEEMKRVGSLIATVLRARTDEVVREVRQQVRELCAAFVPP 420 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: 558 Number of extensions: 31 Number of successful extensions: 5 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: 424 Length adjustment: 31 Effective length of query: 376 Effective length of database: 393 Effective search space: 147768 Effective search space used: 147768 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 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