Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate Ac3H11_2921 Serine hydroxymethyltransferase (EC 2.1.2.1)
Query= BRENDA::B4ECY9 (415 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2921 Length = 414 Score = 648 bits (1671), Expect = 0.0 Identities = 322/415 (77%), Positives = 358/415 (86%), Gaps = 1/415 (0%) Query: 1 MFDRAQSTIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGY 60 M+DR + DPE+FAAI+ EN RQE HIELIASENY SPAVM AQG+QLTNKYAEGY Sbjct: 1 MYDR-NILVEQTDPEVFAAIQAENARQEHHIELIASENYASPAVMWAQGTQLTNKYAEGY 59 Query: 61 PGKRYYGGCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGM 120 PGKRYYGGCE+VDV EQLAIDRVK++FGA+AANVQP+ G+ AN+ VF A LKPGDTIMGM Sbjct: 60 PGKRYYGGCEHVDVAEQLAIDRVKKIFGADAANVQPHCGASANEAVFLAFLKPGDTIMGM 119 Query: 121 SLAHGGHLTHGSPVNMSGKWFNVVSYGLNENEDIDYDAAEKLANEHKPKLIVAGASAFAL 180 SLA GGHLTHG P+NMSGKWFNVVSYGL++NE IDYDA E A EHKPKLIVAGASA++L Sbjct: 120 SLAEGGHLTHGMPLNMSGKWFNVVSYGLDKNEAIDYDAMEAKAREHKPKLIVAGASAYSL 179 Query: 181 KIDFERLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVI 240 IDFER AKIAK +GA MVDMAHYAGLIAAGVYPNPVPHAD VT+TTHKSLRGPRGG+I Sbjct: 180 HIDFERFAKIAKEIGAIFMVDMAHYAGLIAAGVYPNPVPHADVVTSTTHKSLRGPRGGII 239 Query: 241 LMKAEYEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETL 300 LMKAE+EK INSAIFPG+QGGPLMHVIAAKAVAFKEA+ PEFK YQ++V +NA+V+AETL Sbjct: 240 LMKAEHEKAINSAIFPGLQGGPLMHVIAAKAVAFKEAMQPEFKAYQEQVAKNAKVVAETL 299 Query: 301 VKRGLRIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGI 360 RGLRIVSG T+SHVMLVDLRAK ITGK AEA LGAAH+T+NKNAIPNDPEKP VTSG+ Sbjct: 300 TARGLRIVSGGTQSHVMLVDLRAKGITGKEAEAVLGAAHMTINKNAIPNDPEKPMVTSGV 359 Query: 361 RLGSPAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVYR 415 R+G+PAMTTRGF EA NLIADVL+NP D A I VRA+V LT RFPVYR Sbjct: 360 RIGTPAMTTRGFKEEEARITANLIADVLDNPRDEANIAAVRAKVNALTARFPVYR 414 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: 612 Number of extensions: 14 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: 414 Length adjustment: 31 Effective length of query: 384 Effective length of database: 383 Effective search space: 147072 Effective search space used: 147072 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 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