Align Glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_086510497.1 BZY95_RS13805 serine hydroxymethyltransferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2685 (418 letters) >NCBI__GCF_002151265.1:WP_086510497.1 Length = 432 Score = 603 bits (1554), Expect = e-177 Identities = 308/414 (74%), Positives = 350/414 (84%), Gaps = 5/414 (1%) Query: 8 IKGYDDELLAAMNAEDARQEHHIELIASENYTSQRVMQAQGSGLTNKYAEGYPGKRYYGG 67 + +D ++ AA+ E ARQE H+ELIASENY S+ VM+AQG+ LTNKYAEGYPGKRYYGG Sbjct: 6 LAAFDSQVAAAIADEVARQEAHVELIASENYASRAVMEAQGTQLTNKYAEGYPGKRYYGG 65 Query: 68 CEHVDVVEQLAIDRARQLFGADYANVQPHSGSQANAAVYLALLQAGDTVLGMSLAHGGHL 127 CEHVDVVE+LAI+RA LFGAD+ANVQPHSG+QANAAV++AL+ GDTVLGMSLAHGGHL Sbjct: 66 CEHVDVVEKLAIERACDLFGADFANVQPHSGAQANAAVFMALVSPGDTVLGMSLAHGGHL 125 Query: 128 THGAKVSFSGKLYNAVQYGIDTTTGLIDYDEVERLAVEHKPKMIIAGFSAYSKTLDFPRF 187 THGA +FSGK Y+AVQYG++ TG IDY+EVERLA HKPK+IIAGFSAYS+ +D+ RF Sbjct: 126 THGAAPNFSGKHYHAVQYGLNPETGEIDYEEVERLARSHKPKLIIAGFSAYSRVVDWRRF 185 Query: 188 RQIADKVGAYFFVDMAHVAGLVATGLYPNPLPYADVVTTTTHKTLRGPRGGLIL-AKANP 246 R IAD+VGA+ VDMAHVAGLVA GLYP+P+P+A VVTTTTHKTLRGPRGGLIL A + Sbjct: 186 RNIADEVGAWLMVDMAHVAGLVAAGLYPSPVPHAHVVTTTTHKTLRGPRGGLILSAHGDA 245 Query: 247 ELEKKLNAAVFPGGQGGPLMHVIAAKAVCFKEALEPAFKTYQSQVIRNAQAMAQVFIERG 306 EL KKLN AVFPG QGGPLMHVIAAKAV FKEA+ AF YQ +VI NA+AMA+VF+ERG Sbjct: 246 ELYKKLNGAVFPGQQGGPLMHVIAAKAVAFKEAMSQAFVQYQQRVIDNARAMAKVFVERG 305 Query: 307 YDVVSGGTDNHLFLVSLIRQGLTGKDADAALGRAGITVNKNAVPNDPQSPFVTSGLRIGT 366 YDVVSGGTD+HLFLVSLIRQG+TGKDADAALGRA ITVNKNAVPNDPQSPFVTSGLRIGT Sbjct: 306 YDVVSGGTDDHLFLVSLIRQGVTGKDADAALGRAHITVNKNAVPNDPQSPFVTSGLRIGT 365 Query: 367 PAITSRGFKEAQSIALAGWICDILDHL---GDAD-IEANVARQAAALCADFPVY 416 PA+TSRGF A ALAGWICDILD L G+ D +EA V + A LC PVY Sbjct: 366 PAVTSRGFDVADCEALAGWICDILDVLAEQGNTDAVEAEVRTKVAELCERHPVY 419 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: 664 Number of extensions: 27 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: 418 Length of database: 432 Length adjustment: 32 Effective length of query: 386 Effective length of database: 400 Effective search space: 154400 Effective search space used: 154400 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 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