Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate 3608723 Dshi_2115 sarcosine oxidase, alpha subunit family (RefSeq)
Query= curated2:Q67N36 (375 letters) >FitnessBrowser__Dino:3608723 Length = 1000 Score = 149 bits (375), Expect = 4e-40 Identities = 122/400 (30%), Positives = 189/400 (47%), Gaps = 49/400 (12%) Query: 3 ESLKRTPLYELHLKLGARMVPFG----GWEMPV----QYSSVIEEHRAVREAAGLFDVSH 54 E ++TP+ + GA P W P + +V E ++ RE+ G+FD S Sbjct: 607 EVTRKTPIDPWAEEHGAAFEPVALWRRAWYFPQAGEDMHKAVARECKSTRESVGMFDAST 666 Query: 55 MGEFEVRGPQALDLIQLVSTNDAAKLAVGRVQYALMCYENGTVVDDILIYRLDEHRYWLV 114 +G+ EV GP A++ + + TN KL VGR +Y L+ E+G + DD +I R+ + + + Sbjct: 667 LGKIEVSGPDAVEFMNRMYTNPWTKLGVGRCRYGLLLGEDGFIRDDGVIGRMRDDLFHVT 726 Query: 115 VNAG------NTQKDW---EWINTARERAGLHNLELIDRSAEIALLALQGPKAEEILQPL 165 G N +D+ EW + L + E A +AL GP A ++L P Sbjct: 727 TTTGGAARVLNMMEDYLQTEWPEL--------KVWLTSTTEEWATIALNGPNARKLLAPF 778 Query: 166 ATGVVLS-QLEPFSLAKNVTVSGVPTLVLSRTGYTGEDGFEIYVKAEDVAALWEALLEAG 224 G +S P TV+G P+ L R +TGE GFEI V A ALWE L EAG Sbjct: 779 VEGADISADAFPHMSVVECTVAGFPSR-LFRISFTGELGFEINVPARHGKALWEKLWEAG 837 Query: 225 DEQGLLPCGLGARDTLRFEAKLPLYGHEISDQHNPLEAGLGFAVKLKKGVDFIGRDALAR 284 + + P G LR E + G + P +AG+G+A+ K DF+G+ +L R Sbjct: 838 QQYDICPYGTETMHVLRAEKGYIIVGQDTDGTVTPQDAGIGWAIG-KAKPDFVGKRSLQR 896 Query: 285 IKEQGPTRK-LVGI-------------EMIDRGVPRQGYPVAVGGEVVGEVTTGSFSPTL 330 P RK LVG+ +++D P+Q P+ +++G VT+ +S TL Sbjct: 897 PDIVAPGRKQLVGLLTEDPKTVLAEGAQIVDD--PKQAKPM----KMIGHVTSSYWSETL 950 Query: 331 EKNIALAYVPVAHSAVGTEVEVIIR-GRALKARVVETPFY 369 ++IA+A V + + + + G A+ A+V T FY Sbjct: 951 GRSIAMAVVEGGFDRMDSTLHIPTESGDAVPAKVTGTVFY 990 Lambda K H 0.319 0.137 0.402 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: 820 Number of extensions: 46 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: 375 Length of database: 1000 Length adjustment: 37 Effective length of query: 338 Effective length of database: 963 Effective search space: 325494 Effective search space used: 325494 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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