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 CA265_RS19165 CA265_RS19165 serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__Pedo557:CA265_RS19165 Length = 423 Score = 468 bits (1203), Expect = e-136 Identities = 234/419 (55%), Positives = 301/419 (71%), Gaps = 16/419 (3%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 D +I+E I KE RQ + LELIASENF S VMEA GSV+TNKYAEGLP KRYYGGC+ V Sbjct: 4 DNQIFELIDKELNRQEHGLELIASENFVSKQVMEAAGSVLTNKYAEGLPGKRYYGGCQVV 63 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 D+ E +AI+RAK LF A NVQPHSG QAN AV +A+L+PGD I+G DLSHGGHLTHG+ Sbjct: 64 DVVEQIAIDRAKELFGAAWVNVQPHSGAQANAAVMLAILQPGDKILGFDLSHGGHLTHGS 123 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 VNFSGK+Y ++YGV ET LIDY +L +A KPKLI+ GASAY R D+A +R +A Sbjct: 124 PVNFSGKLYQPLFYGVEKETGLIDYKKLEEVALAEKPKLIICGASAYSREWDYAFIRSVA 183 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFAKD-- 245 D +GA ++ D++H AGLIA G+ NP+P+ H VT+TTHKTLRGPR G I+ ++F Sbjct: 184 DKIGALVLADISHPAGLIAKGLLANPLPHCHIVTTTTHKTLRGPRGGMIMMGQDFENPWG 243 Query: 246 --------------IDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARV 291 +D +VFPG QGGPL H+IAAKA+AF EA+S+E+ Y +QV ANA+ Sbjct: 244 LKTPKGEIRLMSNLLDMAVFPGTQGGPLEHIIAAKAIAFGEALSEEYGTYIKQVAANAQA 303 Query: 292 LAEEFIKEGFKVVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPV 351 +A+ F+ +G+ ++SGGTD+H++L+DLR+ +TG+ E AL KA ITVNKN VPFD P Sbjct: 304 MAKAFVAKGYGIISGGTDNHLMLIDLRNKNITGKVAENALEKAEITVNKNMVPFDDKSPF 363 Query: 352 KTSGIRLGTPAMTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 TSGIR+GT A+TTRG+KE +M I LI +V+ N DE + V+ EVI++ FPLY Sbjct: 364 VTSGIRVGTAAITTRGLKETEMEKIVDLIDQVLTNPEDEANLNSVKAEVIKLVSAFPLY 422 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: 555 Number of extensions: 26 Number of successful extensions: 2 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: 423 Length adjustment: 32 Effective length of query: 395 Effective length of database: 391 Effective search space: 154445 Effective search space used: 154445 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