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 206642 DVU1203 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >MicrobesOnline__882:206642 Length = 412 Score = 501 bits (1291), Expect = e-146 Identities = 251/410 (61%), Positives = 306/410 (74%) Query: 1 MRHLFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRY 60 M L D E+ +AI+ E ERQ LELIASENF S AV +AQGSV+T+KYAEG P KRY Sbjct: 1 MDELLLQDPEVGKAIILEIERQTGKLELIASENFVSAAVRQAQGSVLTHKYAEGYPGKRY 60 Query: 61 YGGCEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHG 120 YGGCEFVDIAE++AIERA+ +F E+ANVQPHSG+QANM VY A LKPGDTI+GM+LSHG Sbjct: 61 YGGCEFVDIAENIAIERARTIFGCEYANVQPHSGSQANMGVYFACLKPGDTILGMNLSHG 120 Query: 121 GHLTHGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDW 180 GHLTHG+ VNFSG+++N V+YGV ET IDY+Q+ LA+EHKP LIV GASAYPR ID+ Sbjct: 121 GHLTHGSPVNFSGRLFNVVFYGVEKETGRIDYEQVAALAREHKPSLIVAGASAYPRTIDF 180 Query: 181 AKLREIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKK 240 A+ R IAD VGA LMVDMAH AGL+A G +P+PV +AH+ T+TTHKTLRGPR G IL + Sbjct: 181 ARFRAIADEVGAKLMVDMAHIAGLVAAGYHPSPVQHAHYTTTTTHKTLRGPRGGMILSTE 240 Query: 241 EFAKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEG 300 + K ++ +FPGIQGGPLMHVIAAKAVAF EA+ FKEY +QVV NA LA G Sbjct: 241 DNGKTLNSQIFPGIQGGPLMHVIAAKAVAFGEALRPAFKEYQKQVVDNAAALAGVLTAAG 300 Query: 301 FKVVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGT 360 F +VSGGTD+H++L+DL +TG++ E AL KA ITVNKN VPF+ P TSG+RLGT Sbjct: 301 FDLVSGGTDNHLMLVDLTSKDVTGKDAEIALDKAGITVNKNTVPFETRSPFVTSGVRLGT 360 Query: 361 PAMTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 PA+TTRGMK +M + I I N +E + + +EV QFPL+ Sbjct: 361 PALTTRGMKAAEMEKVGGWIVDAIANTTNETRLAEISREVERFARQFPLF 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: 592 Number of extensions: 23 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: 412 Length adjustment: 32 Effective length of query: 395 Effective length of database: 380 Effective search space: 150100 Effective search space used: 150100 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 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