Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1; L-threonine/L-allo-threonine aldolase; EC 4.1.2.48 (uncharacterized)
to candidate BPHYT_RS25180 BPHYT_RS25180 serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__BFirm:BPHYT_RS25180 Length = 424 Score = 471 bits (1212), Expect = e-137 Identities = 242/413 (58%), Positives = 300/413 (72%), Gaps = 6/413 (1%) Query: 4 LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63 L D + AI+KE ERQ +ELIASEN S AV+EAQGSV+TNKYAEG P KRYYGG Sbjct: 12 LATRDTAVRGAILKELERQQSQVELIASENIVSRAVLEAQGSVLTNKYAEGYPGKRYYGG 71 Query: 64 CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123 CE+ D+ E LA++R K LF+A+ ANVQPHSG QAN AV +A++KPGDT++GM L GGHL Sbjct: 72 CEYADVVETLALDRIKQLFNAKFANVQPHSGAQANGAVMLALVKPGDTVLGMSLDAGGHL 131 Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183 THGAK SGK +NAV YGV+ +T LIDY+Q+ LA++H+P L++ G SAYPR +D+A+L Sbjct: 132 THGAKPAMSGKWFNAVQYGVNRDTMLIDYEQIEVLAQQHQPALLIAGFSAYPRALDFARL 191 Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKE-F 242 R I DSVGA LMVDMAH AG+IA G + NPV YAH VTSTTHKTLRGPR GF+L E Sbjct: 192 RAIVDSVGAKLMVDMAHIAGIIAAGRHQNPVEYAHVVTSTTHKTLRGPRGGFVLTNDEDI 251 Query: 243 AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFK 302 AK I+ +VFPG+QGGPLMHVIA KAVAF EA+ FK Y V+ANA+ L E G Sbjct: 252 AKKINSAVFPGLQGGPLMHVIAGKAVAFGEALEPGFKTYIDSVLANAQALGEVLKAGGVD 311 Query: 303 VVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPA 362 +V+GGTD+H++L+DLR GL G +VE+AL +A IT NKN +PFD P TSGIRLGTPA Sbjct: 312 LVTGGTDNHLLLVDLRPKGLKGNQVEQALERAGITCNKNGIPFDTEKPTVTSGIRLGTPA 371 Query: 363 MTTRGMKEDQMRIIARLISKVIKNI-----GDEKVIEYVRQEVIEMCEQFPLY 410 TTRG + R I RLI +V+ + G + VR+E+ +CE+FP+Y Sbjct: 372 GTTRGFGVSEFREIGRLIVEVLDALRDHPEGHAATEQRVRREIFALCERFPIY 424 Lambda K H 0.319 0.136 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: 589 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: 427 Length of database: 424 Length adjustment: 32 Effective length of query: 395 Effective length of database: 392 Effective search space: 154840 Effective search space used: 154840 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 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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