Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate GFF1886 PGA1_c19150 sarcosine oxidase subunit alpha
Query= curated2:C3PHK3 (370 letters) >FitnessBrowser__Phaeo:GFF1886 Length = 1010 Score = 158 bits (400), Expect = 6e-43 Identities = 107/355 (30%), Positives = 176/355 (49%), Gaps = 29/355 (8%) Query: 7 SPLHAEHEKLGATFTPFGPWEMPLKYDNELEE-----HRAVRNAA---GLFDLSHMGEIW 58 +P+H H+ GA + P G W P Y E +R V+N GL D S +G++ Sbjct: 619 TPMHDWHDSNGADWEPVGQWRRPFAYVRSGESLHDAVNREVKNTRENLGLLDASTLGKLV 678 Query: 59 VNGPDAAEFLSYCFISNLTTLKEGKAKYSMICAEDGGIIDDLITYRLEETKFLVVPNAGN 118 V GPDA +FL + + ++TLK GK +Y ++C+E+G +IDD + R++E +L G Sbjct: 679 VKGPDAGKFLDMMYTNMMSTLKIGKCRYGLMCSENGFLIDDGVVARIDEDTWLCHTTTGG 738 Query: 119 ADTVWDALNE--RAEGFD--VDLKNESRDVAMIAVQGPKALEILVPLVE------DTKQQ 168 A+ + + E + E +D V + N + +A +AV GP A ++L L E D ++ Sbjct: 739 AERIHGHMEEWLQTEWWDWKVYVANITEQLAQVAVVGPNARKVLEKLNENAGGGMDLSKE 798 Query: 169 AVMDLPYYAAMTGKVARKYAFICRTGYTGEDGFELIVYNSDAPELWEELLKAGEEYGIKP 228 A LP+ G++ A R ++GE +E+ V SD W L++AG+E+G+ P Sbjct: 799 A---LPFMEWRDGEIGGFKARAYRISFSGELSYEIAVAASDGQAFWTALMEAGKEFGVMP 855 Query: 229 CGLAARDSLRLEAGMPLYGNELTRDITPVEAGMSRAFAKKEQDFVGAEV-LRQRAEEGPQ 287 G LR E G + G+E + P + G++ A +KK++DF+G R + + Sbjct: 856 YGTECLHILRAEKGFIMIGDETDGTVIPQDLGLNWALSKKKEDFLGKRAHTRSHMADPDR 915 Query: 288 AVITGLVSSQ-------RRAARAGSEVYVGENKVGTVTSGQPSPTLGHPVALALI 335 + GL ++ A G +N +G VTS S LG +A+ L+ Sbjct: 916 WQLVGLETTDGSVLPDGAYAVGNGVNANGQKNTIGRVTSTYYSSNLGRGIAMGLV 970 Lambda K H 0.316 0.135 0.398 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: 896 Number of extensions: 34 Number of successful extensions: 4 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: 370 Length of database: 1010 Length adjustment: 37 Effective length of query: 333 Effective length of database: 973 Effective search space: 324009 Effective search space used: 324009 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: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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