Align Serine hydroxymethyltransferase; SHMT; Serine methylase; L-threonine/L-allo-threonine aldolase; EC 2.1.2.1; EC 4.1.2.48 (characterized)
to candidate WP_092349909.1 BLU87_RS14030 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_900107645.1:WP_092349909.1 Length = 415 Score = 546 bits (1407), Expect = e-160 Identities = 270/410 (65%), Positives = 325/410 (79%) Query: 1 MRHLFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRY 60 M +L + D EI++ I KE +RQ Y+LE IASENF S AVMEAQGSV+TNKYAEG P KRY Sbjct: 1 MSNLKDFDPEIFQVINKETQRQEYNLEFIASENFVSEAVMEAQGSVLTNKYAEGYPSKRY 60 Query: 61 YGGCEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHG 120 YGGCEFVD+AE LAI+RAK LF AEH NVQPHSG+QANMAVYMAV KPGDTI+GM+L+HG Sbjct: 61 YGGCEFVDVAEQLAIDRAKELFGAEHVNVQPHSGSQANMAVYMAVCKPGDTILGMNLAHG 120 Query: 121 GHLTHGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDW 180 GHLTHG+ VNFSGK+YN V YG+ ET IDY+++ RLAKEH+PKLIV GASAYPR ID+ Sbjct: 121 GHLTHGSSVNFSGKLYNIVPYGLSAETGTIDYEEVERLAKEHQPKLIVVGASAYPREIDF 180 Query: 181 AKLREIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKK 240 R IADSVGA +MVDMAH AGL+A G++ NPVPYA FVT+TTHKTLRGPR G ILC + Sbjct: 181 PAFRRIADSVGAAVMVDMAHIAGLVAAGIHSNPVPYAEFVTTTTHKTLRGPRGGMILCTE 240 Query: 241 EFAKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEG 300 E+ K I+ S+FPGIQGGPLMHVIAAKAVAFKEA+ EFK+YA QVV NA+ LA + +G Sbjct: 241 EWGKKINSSIFPGIQGGPLMHVIAAKAVAFKEALRPEFKDYAAQVVKNAQALAGALVDKG 300 Query: 301 FKVVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGT 360 + +VSGGTD+H++L+D T +TG+ E+ L A ITVNKNAVPFD P TSGIR+GT Sbjct: 301 YNLVSGGTDNHLMLVDFTGTDITGKVAEKTLEDAGITVNKNAVPFDSRSPFITSGIRVGT 360 Query: 361 PAMTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 PA TTRG+KE MR +A I + ++NI + + +R EV E+C +FPLY Sbjct: 361 PATTTRGLKEADMRQVAEWIDRALQNIDNAAALATIRAEVKELCLRFPLY 410 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: 26 Number of successful extensions: 1 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: 415 Length adjustment: 32 Effective length of query: 395 Effective length of database: 383 Effective search space: 151285 Effective search space used: 151285 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: 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