Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate Dsui_1265 Dsui_1265 glycine/serine hydroxymethyltransferase
Query= BRENDA::B4ECY9 (415 letters) >FitnessBrowser__PS:Dsui_1265 Length = 416 Score = 646 bits (1666), Expect = 0.0 Identities = 323/411 (78%), Positives = 357/411 (86%), Gaps = 1/411 (0%) Query: 5 AQSTIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGYPGKR 64 A T+A VDPE++ AIE ENRRQE+HIELIASENY S AVM AQGSQLTNKYAEGYPGKR Sbjct: 4 ANDTLAKVDPELWKAIEDENRRQEEHIELIASENYVSNAVMEAQGSQLTNKYAEGYPGKR 63 Query: 65 YYGGCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAH 124 YYGGCEYVDV EQLAI+R+K+LFGAEAANVQPNSGSQANQ V A KPGDTIMGMSLA Sbjct: 64 YYGGCEYVDVAEQLAIERLKKLFGAEAANVQPNSGSQANQAVLMAFAKPGDTIMGMSLAE 123 Query: 125 GGHLTHGSPVNMSGKWFNVVSYGLNENEDIDYDAAEKLANEHKPKLIVAGASAFALKIDF 184 GGHLTHG +NMSGKWFNVVSYGLNE E+IDYD E LA EHKPK+IVAGASA+AL+IDF Sbjct: 124 GGHLTHGMALNMSGKWFNVVSYGLNEKEEIDYDKMEALAREHKPKIIVAGASAYALRIDF 183 Query: 185 ERLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKA 244 ER AKIAK VGA VDMAHYAGLIAAG YPNPVP AD VT+TTHK+LRGPRGGVILMKA Sbjct: 184 ERFAKIAKEVGAIFWVDMAHYAGLIAAGYYPNPVPFADVVTSTTHKTLRGPRGGVILMKA 243 Query: 245 EYEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETL-VKR 303 E+EK +NSAIFPG+QGGPLMHVIAAKAVAFKEA SPEFK+YQ++V+ NARV+A+ L +R Sbjct: 244 EHEKALNSAIFPGLQGGPLMHVIAAKAVAFKEAASPEFKKYQEQVINNARVMAKVLGEER 303 Query: 304 GLRIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLG 363 GLRIVSGRTESHV L+DLRAK ITGK AEAALG AHITVNKN IPNDPEKPFVTSGIR+G Sbjct: 304 GLRIVSGRTESHVFLIDLRAKKITGKEAEAALGKAHITVNKNGIPNDPEKPFVTSGIRIG 363 Query: 364 SPAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVY 414 SPAMT+RGF EAEQ+ +L+ADVL+ P D A + VRA+VA L +FPVY Sbjct: 364 SPAMTSRGFTEIEAEQIAHLVADVLDAPNDEAKLAEVRAKVAALCAKFPVY 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: 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: 415 Length of database: 416 Length adjustment: 31 Effective length of query: 384 Effective length of database: 385 Effective search space: 147840 Effective search space used: 147840 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