Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_101444761.1 BD749_RS11795 serine hydroxymethyltransferase
Query= BRENDA::I7H6W6 (427 letters) >NCBI__GCF_002846395.1:WP_101444761.1 Length = 424 Score = 468 bits (1205), Expect = e-136 Identities = 242/429 (56%), Positives = 299/429 (69%), Gaps = 25/429 (5%) Query: 10 LQTDPTISGMMQKELQRQREHLELIASENFTSPAVMATQGSVLTNKYAEGLPKKRYYGGC 69 +Q D I ++ KE RQ +ELIASENF S VM GSV+TNKYAEGLP KRYYGGC Sbjct: 1 MQKDTAIFDLIAKEKARQTHGIELIASENFVSDQVMQAMGSVMTNKYAEGLPGKRYYGGC 60 Query: 70 EFIDEIEQVAIDRAKELFGAASANVQPHSGAQANFAVFLTLLKPGDKIMGMDLSHGGHLT 129 E +D+ EQ+AIDRAKELFGA NVQPHSGAQAN AV L +L+PGDKI+G DLSHGGHLT Sbjct: 61 EIVDQSEQLAIDRAKELFGATWVNVQPHSGAQANSAVMLAVLQPGDKILGFDLSHGGHLT 120 Query: 130 HGSPANVSGKWFEAVHYGVSQETEQLDYDHILEVARQERPKLIICGYSAYPRIINFEKFR 189 HGSP N SGK ++ YGV QET +D+D ++E AR+E+PKLIICG SAY R +++K R Sbjct: 121 HGSPVNFSGKLYQPSFYGVEQETGLIDFDKVVETARREKPKLIICGASAYSRDWDYKKLR 180 Query: 190 AIADEVGAYLLADIAHIAGLVASGHHPNPVPHCDVVTTTTHKTLRGPRGGLILTRDPELG 249 A ADEVGA LLADI+H +GL+A G NP HC +VTTTTHKTLRGPRGG+I+ +G Sbjct: 181 AAADEVGALLLADISHPSGLIAKGLLNNPFEHCHIVTTTTHKTLRGPRGGMIM-----MG 235 Query: 250 KKFNK--------------------SVFPGTQGGPLEHVIAGKAVAFGEALKPEFKAYSG 289 K F +VFPGTQGGPLEHVIA KAVA+ EAL ++ Y Sbjct: 236 KDFENPFGLKTPKGEIRMMSSLLDGAVFPGTQGGPLEHVIAAKAVAYYEALSDDYMGYIK 295 Query: 290 QVIANAQAMAQQLQNRGFKIVSGGTDNHLMLVDLRSVNLTGKQADQLVSDVNITANKNTV 349 QV NAQAMA RG+ I+SGGTDNH+ML+DLRS LTGK A+ + +IT NKN V Sbjct: 296 QVQQNAQAMANAFVERGYNIISGGTDNHMMLIDLRSKGLTGKLAENTLVKADITINKNMV 355 Query: 350 PFDPESPFVTSGLRLGSPAMTTRGLGTEDFAEIANIIADRLQNPEDEQVKQACVQRVAAL 409 PFD +SPFVTSG+R+G+ A+TTRGL D A I +I D L N +++ +A + V + Sbjct: 356 PFDDKSPFVTSGMRVGTAAITTRGLKETDMARIVELIDDVLTNNDNDSKIEAVRKEVNSW 415 Query: 410 CERFPLYPH 418 +++PL+ + Sbjct: 416 MQQYPLFAY 424 Lambda K H 0.318 0.134 0.393 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: 546 Number of extensions: 17 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: 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 ( 7.3 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 Jul 26 2024. The underlying query database was built on Jul 25 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