Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_012405154.1 BPHY_RS29645 serine hydroxymethyltransferase
Query= BRENDA::B4ECY9 (415 letters) >NCBI__GCF_000020045.1:WP_012405154.1 Length = 438 Score = 584 bits (1505), Expect = e-171 Identities = 291/411 (70%), Positives = 348/411 (84%), Gaps = 1/411 (0%) Query: 6 QSTIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGYPGKRY 65 ++T+A DPE+ AI E +RQ+DHIELIASENYTSPAV+ AQGSQLTNKYAEGYPGKRY Sbjct: 5 KNTLAVTDPELQHAIAAETQRQQDHIELIASENYTSPAVLEAQGSQLTNKYAEGYPGKRY 64 Query: 66 YGGCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAHG 125 YGGCE+VDVVEQLAIDR KQLF A+ ANVQP+SGSQANQ V+ + L PGDTI+GMSLAHG Sbjct: 65 YGGCEHVDVVEQLAIDRAKQLFNADHANVQPHSGSQANQAVYLSALTPGDTILGMSLAHG 124 Query: 126 GHLTHGSPVNMSGKWFNVVSYGLN-ENEDIDYDAAEKLANEHKPKLIVAGASAFALKIDF 184 GHLTHG+ VN+SGK FN VSYGL+ E E+IDYD A++LA +H+P++IVAGASA++L ID+ Sbjct: 125 GHLTHGASVNVSGKLFNAVSYGLDAETEEIDYDTAQRLAEQHRPRMIVAGASAYSLVIDW 184 Query: 185 ERLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKA 244 +R IA SVGA L+VDMAHYAGL+AAG+YP+PV AD+VTTTTHK+LRGPRGG+IL +A Sbjct: 185 QRFRAIADSVGATLLVDMAHYAGLVAAGLYPSPVGIADYVTTTTHKTLRGPRGGLILSRA 244 Query: 245 EYEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLVKRG 304 E K I+S IFPGIQGGPLMHVIA KA A +EA++ EF++YQQ+V+ NAR +A+TL +RG Sbjct: 245 ETAKAIDSTIFPGIQGGPLMHVIAGKAAALREAMTDEFRQYQQQVLVNARTIAQTLQQRG 304 Query: 305 LRIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLGS 364 LRIVSGRT+SHV LVDLRAK++TGK AEAALG A ITVNKNAIPNDP+KPFVTSG+R+GS Sbjct: 305 LRIVSGRTDSHVFLVDLRAKNVTGKEAEAALGRAFITVNKNAIPNDPQKPFVTSGVRIGS 364 Query: 365 PAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVYR 415 PA+TTRG AEAEQ+ +LIADVL+ P + I R V LT RFPVYR Sbjct: 365 PAITTRGLREAEAEQLAHLIADVLDAPGNDLVIRRTADAVLALTARFPVYR 415 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: 563 Number of extensions: 14 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: 415 Length of database: 438 Length adjustment: 32 Effective length of query: 383 Effective length of database: 406 Effective search space: 155498 Effective search space used: 155498 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 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