Align Glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_086509415.1 BZY95_RS07965 serine hydroxymethyltransferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2685 (418 letters) >NCBI__GCF_002151265.1:WP_086509415.1 Length = 421 Score = 621 bits (1602), Expect = 0.0 Identities = 316/422 (74%), Positives = 357/422 (84%), Gaps = 6/422 (1%) Query: 1 MFSKHDQIKGYDDELLAAMNAEDARQEHHIELIASENYTSQRVMQAQGSGLTNKYAEGYP 60 MFS+ I G+DD L AM E ARQE HIELIASENY S RV++AQGS LTNKYAEGYP Sbjct: 1 MFSRDMTIAGFDDALFDAMQKEVARQEAHIELIASENYASPRVLEAQGSQLTNKYAEGYP 60 Query: 61 GKRYYGGCEHVDVVEQLAIDRARQLFGADYANVQPHSGSQANAAVYLALLQAGDTVLGMS 120 GKRYYGGCE+VD+VEQLAID A+QLF A YANVQPHSGSQAN+AV+ AL++ GDTVLGMS Sbjct: 61 GKRYYGGCEYVDIVEQLAIDYAKQLFAASYANVQPHSGSQANSAVFQALVKPGDTVLGMS 120 Query: 121 LAHGGHLTHGAKVSFSGKLYNAVQYGIDTTTGLIDYDEVERLAVEHKPKMIIAGFSAYSK 180 L GGHLTHGAK +FSGK YNAVQYGID G IDY+EV RLA EH+PKMIIAGFSAYS+ Sbjct: 121 LDAGGHLTHGAKPNFSGKHYNAVQYGIDGN-GRIDYEEVARLAREHQPKMIIAGFSAYSQ 179 Query: 181 TLDFPRFRQIADKVGAYFFVDMAHVAGLVATGLYPNPLPYADVVTTTTHKTLRGPRGGLI 240 +D+ RFR+IAD+VGAY VDMAH+AGLVA G+YP+PLP+A VVTTTTHKTLRGPRGGLI Sbjct: 180 IIDWARFRKIADEVGAYLLVDMAHIAGLVAAGVYPSPLPHAHVVTTTTHKTLRGPRGGLI 239 Query: 241 L-AKANPELEKKLNAAVFPGGQGGPLMHVIAAKAVCFKEALEPAFKTYQSQVIRNAQAMA 299 L A+ N E+EKKL +AVFPGGQGGPL HVIAAKAVCFKEA+EP FK+YQ QV++NAQ MA Sbjct: 240 LSAEGNEEIEKKLQSAVFPGGQGGPLEHVIAAKAVCFKEAMEPGFKSYQQQVVKNAQTMA 299 Query: 300 QVFIERGYDVVSGGTDNHLFLVSLIRQGLTGKDADAALGRAGITVNKNAVPNDPQSPFVT 359 VFIERGYD+VSGGT++HLFL+SLI+QGLTGKDADAALGRA ITVNKNAVP DPQSPFVT Sbjct: 300 GVFIERGYDIVSGGTEDHLFLLSLIKQGLTGKDADAALGRAHITVNKNAVPGDPQSPFVT 359 Query: 360 SGLRIGTPAITSRGFKEAQSIALAGWICDILDHLG----DADIEANVARQAAALCADFPV 415 SGLRIGTPA+T+RGF E + LAGWICDILD + A IEA V + A+CA FPV Sbjct: 360 SGLRIGTPAVTTRGFGEGECRELAGWICDILDVMAKGEDTAAIEAEVKDKVEAVCARFPV 419 Query: 416 YR 417 YR Sbjct: 420 YR 421 Lambda K H 0.319 0.135 0.395 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: 681 Number of extensions: 26 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: 418 Length of database: 421 Length adjustment: 32 Effective length of query: 386 Effective length of database: 389 Effective search space: 150154 Effective search space used: 150154 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