Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate 350266 BT0738 serine hydroxymethyltransferase (NCBI ptt file)
Query= BRENDA::Q5HE87 (412 letters) >FitnessBrowser__Btheta:350266 Length = 426 Score = 471 bits (1212), Expect = e-137 Identities = 239/423 (56%), Positives = 304/423 (71%), Gaps = 17/423 (4%) Query: 6 KQDKVIAEAIEREFQRQNSNIELIASENFVSEAVMEAQGSVLTNKYAEGYPGRRYYGGCE 65 K+D +I + IE+E QRQ IELIASENFVS+ VM+A GS LTNKYAEGYPG+RYYGGCE Sbjct: 2 KRDDLIFDIIEKEHQRQLKGIELIASENFVSDQVMQAMGSCLTNKYAEGYPGKRYYGGCE 61 Query: 66 FVDVTESIAIDRAKALFGAEHVNVQPHSGSQANMAVYLVALEMGDTVLGMNLSHGGHLTH 125 VD +E IAIDR K +FGAE NVQPHSG+QAN AV+L L GD +G+NL+HGGHL+H Sbjct: 62 VVDQSEQIAIDRLKEIFGAEWANVQPHSGAQANAAVFLAVLNPGDKFMGLNLAHGGHLSH 121 Query: 126 GAPVNFSGKFYNFVEYGVDKDTERINYDEVRKLALEHKPKLIVAGASAYSRTIDFKKFKE 185 G+ VN SG Y EY ++++T R++YD++ ++AL KPK+I+ G SAYSR D+K+ +E Sbjct: 122 GSLVNTSGIIYTPCEYNLNQETGRVDYDQMEEVALREKPKMIIGGGSAYSREWDYKRMRE 181 Query: 186 IADEVNAKLMVDMAHIAGLVAAGLHPNPVEYADFVTTTTHKTLRGPRGGMILCKEEYKKD 245 IAD+V A LM+DMAH AGL+AAGL NPV+YA VT+TTHKTLRGPRGG+I+ +++ Sbjct: 182 IADKVGAILMIDMAHPAGLIAAGLLENPVKYAHIVTSTTHKTLRGPRGGVIMMGKDFPNP 241 Query: 246 ----------------IDKTIFPGIQGGPLEHVIAAKAVAFGEALENNFKTYQQQVVKNA 289 +D +FPG+QGGPLEHVIAAKAVAFGE L+ +K Y +QV KNA Sbjct: 242 WGKKTPKGEIKMMSQLLDSAVFPGVQGGPLEHVIAAKAVAFGEILQPEYKEYAKQVQKNA 301 Query: 290 KVLAEALINEGFRIVSGGTDNHLVAVDVKGSI-GLTGKEAEETLDSVGITCNKNTIPFDQ 348 +LA+ALI+ GF IVSGGTDNH + VD++ LTGK AE+ L S IT NKN +PFD Sbjct: 302 AILAQALIDRGFTIVSGGTDNHSMLVDLRSKYPDLTGKVAEKALVSADITVNKNMVPFDS 361 Query: 349 EKPFVTSGIRLGTPAATTRGFDEKAFEEVAKIISLALKNSKDEEKLQQAKERVAKLTAEY 408 F TSGIRLGTPA TTRG E E+A++I L N ++EE + Q + RV + +Y Sbjct: 362 RSAFQTSGIRLGTPAITTRGAKEDLMIEIAEMIETVLSNVENEEVIAQVRARVNETMKKY 421 Query: 409 PLY 411 PL+ Sbjct: 422 PLF 424 Lambda K H 0.315 0.133 0.372 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: 523 Number of extensions: 23 Number of successful extensions: 3 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: 412 Length of database: 426 Length adjustment: 32 Effective length of query: 380 Effective length of database: 394 Effective search space: 149720 Effective search space used: 149720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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