Align glycine hydroxymethyltransferase (EC 2.1.2.1); low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate SMc01770 SMc01770 serine hydroxymethyltransferase
Query= BRENDA::P0A825 (417 letters) >FitnessBrowser__Smeli:SMc01770 Length = 431 Score = 497 bits (1280), Expect = e-145 Identities = 250/418 (59%), Positives = 314/418 (75%), Gaps = 10/418 (2%) Query: 7 NIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYPGKRYYG 66 ++AD D E++ A+E+E RQ IELIASEN S V++AQGS +TNKYAEGYPGKRYYG Sbjct: 13 SLADSDPEIFGAIEKELGRQRHEIELIASENIVSRAVLEAQGSIMTNKYAEGYPGKRYYG 72 Query: 67 GCEYVDIVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLEPGDTVLGMNLAHGGH 126 GC+YVDI E LAI+RAK+LFG ++ANVQP+SGSQ N AV+ ALL+PGDT +G++L GGH Sbjct: 73 GCQYVDIAEALAIERAKKLFGVNFANVQPNSGSQMNQAVFLALLQPGDTFMGLDLNSGGH 132 Query: 127 LTHGSPVNFSGKLYNIVPYGIDATGH-IDYADLEKQAKEHKPKMIIGGFSAYSGVVDWAK 185 LTHGSPVN SGK +N+V YG+ H +D ++ ++A+E KPK+II G +AYS + DW + Sbjct: 133 LTHGSPVNMSGKWFNVVSYGVREDDHLLDMDEVARKAREQKPKLIIAGGTAYSRIWDWKR 192 Query: 186 MREIADSIGAYLFVDMAHVAGLVAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGS 245 REIAD +GA+L VDMAH+AGLVA G +P+P PH HV TTTTHK+L GPRGG+IL Sbjct: 193 FREIADEVGAWLMVDMAHIAGLVAGGQHPSPFPHCHVATTTTHKSLRGPRGGMILT--ND 250 Query: 246 EELYKKLNSAVFPGGQGGPLMHVIAGKAVALKEAMEPEFKTYQQQVAKNAKAMVEVFLER 305 EE+ KK+NSAVFPG QGGPLMHVIA KAVAL EA++P FK Y QV KNA+ + E Sbjct: 251 EEIAKKINSAVFPGLQGGPLMHVIAAKAVALGEALQPSFKDYAAQVVKNARTLAETLKAN 310 Query: 306 GYKVVSGGTDNHLFLVDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTSGIRVG 365 G +VSGGTDNHL LVDL KN TGK A+AALGRA +T NKN +P DP+ PFVTSG+R+G Sbjct: 311 GLDIVSGGTDNHLMLVDLRKKNATGKRAEAALGRAYVTCNKNGIPFDPEKPFVTSGVRLG 370 Query: 366 TPAITRRGFKEAEAKELAGWMCDVLDSI----NDE---AVIERIKGKVLDICARYPVY 416 PA T RGFKEAE KE+ + +VLD + +DE AV ++ KV+ + R+P+Y Sbjct: 371 APAGTTRGFKEAEFKEVGELIVEVLDGLKAANSDEGNAAVEAGVREKVIKLTDRFPMY 428 Lambda K H 0.316 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: 575 Number of extensions: 23 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: 417 Length of database: 431 Length adjustment: 32 Effective length of query: 385 Effective length of database: 399 Effective search space: 153615 Effective search space used: 153615 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 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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