Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_050463875.1 AKL27_RS16115 serine hydroxymethyltransferase
Query= BRENDA::B4ECY9 (415 letters) >NCBI__GCF_001189915.1:WP_050463875.1 Length = 415 Score = 686 bits (1771), Expect = 0.0 Identities = 337/407 (82%), Positives = 375/407 (92%) Query: 8 TIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGYPGKRYYG 67 TIAN+DP++++AI++EN RQ++HIELIASENYTSPAVM AQGSQLTNKYAEGYPGKRYYG Sbjct: 7 TIANIDPDLWSAIQKENHRQQEHIELIASENYTSPAVMEAQGSQLTNKYAEGYPGKRYYG 66 Query: 68 GCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAHGGH 127 GCE+VD+ EQLAIDR+KQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLA GGH Sbjct: 67 GCEFVDIAEQLAIDRLKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAEGGH 126 Query: 128 LTHGSPVNMSGKWFNVVSYGLNENEDIDYDAAEKLANEHKPKLIVAGASAFALKIDFERL 187 LTHG +NMSGKWFNVVSYGLN+ E+IDYDA E+LA E KPK+I+AGASA+AL+IDFER Sbjct: 127 LTHGMALNMSGKWFNVVSYGLNDKEEIDYDAMERLAREKKPKMIIAGASAYALRIDFERF 186 Query: 188 AKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKAEYE 247 A+IAK VGAY MVDMAHYAGLIAAGVYPNPVPHADFVT+TTHKSLRGPRGG IL KAE+E Sbjct: 187 ARIAKEVGAYFMVDMAHYAGLIAAGVYPNPVPHADFVTSTTHKSLRGPRGGFILSKAEHE 246 Query: 248 KPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLVKRGLRI 307 K INSAIFPGIQGGPLMHVIA KA+AFKEALSPEFK YQQ+VV+NA LA+TL++RGLRI Sbjct: 247 KAINSAIFPGIQGGPLMHVIAGKAIAFKEALSPEFKTYQQQVVKNADALAKTLIERGLRI 306 Query: 308 VSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLGSPAM 367 VSGRTESHVMLVDLRAK ITGK AEA LG+AH+T NKNAIPNDPEKPFVTSGIR+GSPAM Sbjct: 307 VSGRTESHVMLVDLRAKKITGKEAEAILGSAHMTCNKNAIPNDPEKPFVTSGIRIGSPAM 366 Query: 368 TTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVY 414 TTRGF AEA +V +LIADVL+NP DAATIERV+A+V +LT FPVY Sbjct: 367 TTRGFKEAEAVKVAHLIADVLDNPHDAATIERVKAEVKKLTDAFPVY 413 Lambda K H 0.316 0.132 0.376 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: 616 Number of extensions: 15 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: 415 Length of database: 415 Length adjustment: 31 Effective length of query: 384 Effective length of database: 384 Effective search space: 147456 Effective search space used: 147456 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: 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