Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate WP_084191695.1 U743_RS04135 FAD-dependent oxidoreductase
Query= curated2:O86567 (372 letters) >NCBI__GCF_000733765.1:WP_084191695.1 Length = 947 Score = 173 bits (439), Expect = 2e-47 Identities = 136/379 (35%), Positives = 176/379 (46%), Gaps = 27/379 (7%) Query: 7 RRTALDATHRALGATMTDFAGWDMPLRYGSERE-------EHVAVRTRAGLFDLSHMGEI 59 R T L H+ALGA + W P YG E E AVR+RAGL D+S +G+I Sbjct: 565 RLTPLHEAHQALGAHFMEAGEWLRPAFYGDAAEADSAIAAEVAAVRSRAGLIDVSTLGKI 624 Query: 60 TVTGPQAAELLNFALVGNIGTVKPGRARYTMICREDGGILDDLIVYRLEEAEYMVVANAS 119 V G A LL A + + GR RY ++ G I+DD IV RL E Y V + Sbjct: 625 EVLGADAGRLLEAAYTMRMTNIAVGRTRYALMVDSSGVIVDDGIVGRLAEDRYYVTTTSG 684 Query: 120 NAQVVLDALTERAA--GFDAEVRDDRDAYALLAVQGPESPGILASLTD---ADLDGLKYY 174 +A L+ A G D + + L + GPE+ +LA L D D Y Sbjct: 685 HAAATFRTLSRCALEWGLDVHLLNRTGQLGALNLAGPEARRLLAPLVSDVGLDEDAFPYL 744 Query: 175 AGLPGTVAGVPALIARTGYTGEDGFELFVKPEHAVGLWQALTGAGEAAGLIPCGLSCRDT 234 G V G PA +AR G+ GE G+EL + +WQAL +A P G+ + Sbjct: 745 GIREGRVCGHPARLARVGFVGELGYELHLDARATAEVWQALMRDADAPR--PFGVEAQRL 802 Query: 235 LRLEAGMPLYGNELSTALTPFDAGLGRVVKFEKEGDFVGRAALTEAAERAASRPPRVLVG 294 LRLE G + G + PF+AG+G V F+K F GRAAL + R R LVG Sbjct: 803 LRLEKGHIIVGQDTDGLSDPFEAGMGWAVHFKKP-FFNGRAALQQLKPRMRRR----LVG 857 Query: 295 --LVAEGRRVPRSGYRVVAGGEVIGEVTSGAPSPTLGRPIAMAYVDPAHAAPGTEGVGVD 352 L A +PR + V+ G + G VTS A SPTL P+ +A VD AA G + Sbjct: 858 FALPAGVETLPRECHLVIRDGVIAGRVTSIAHSPTLRHPVGLAMVD---AALADSGEALQ 914 Query: 353 IRGSH---EPYEVVALPFY 368 IRG E A PFY Sbjct: 915 IRGDDGRMHRAEQRATPFY 933 Lambda K H 0.318 0.137 0.400 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: 921 Number of extensions: 55 Number of successful extensions: 5 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: 372 Length of database: 947 Length adjustment: 37 Effective length of query: 335 Effective length of database: 910 Effective search space: 304850 Effective search space used: 304850 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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