Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate 3608080 Dshi_1485 FAD dependent oxidoreductase (RefSeq)
Query= curated2:C1F933 (378 letters) >FitnessBrowser__Dino:3608080 Length = 804 Score = 147 bits (372), Expect = 8e-40 Identities = 105/333 (31%), Positives = 160/333 (48%), Gaps = 10/333 (3%) Query: 42 AEHMAVRTGVGLFDVSHMGDIQLRGPGSLDAVQHICMNDASKLAVGQAHYSAMLYPQGTF 101 AE MAVRTGVG+ ++ + G ++ GPG+ + I A + S ML P G Sbjct: 470 AEVMAVRTGVGINELQNFGKFRVTGPGARAWLDRIMAGRIP--APRRLSLSPMLAPSGRL 527 Query: 102 VDDVIVHKFSDNDYLIVINAGTREKDYEWIRSHAQPFHCHVSNYSDLYTQLAIQGPRAAE 161 + D + S+ ++ + + G ++ W ++H V N SD T I GPRA E Sbjct: 528 IGDFTISCLSETEFQLTASYGAQDYHLRWFQTHLDD-GVTVENISDARTGFQIAGPRARE 586 Query: 162 TLAKLTSVDLAAIKNYRF--TWGTVCNLHNTLIARTGYTGEDGFEIYIPSDEATSERVWN 219 LA T D++A + +RF + + L+ R YTG+ G+EIY E +++ Sbjct: 587 VLAACTRADVSA-EAFRFFDVAPMTIGMAHCLVQRVSYTGDLGYEIYCSPTE--QRHLFH 643 Query: 220 EVLEAGKEFGIVPCGLGARNTLRLESAMALYGHEISQDIDVFEAGLDRYCKLDKGT-FVG 278 + EAG+ GI P G+ A +LRL+ + E S D E GLDR+ K T F+G Sbjct: 644 TLWEAGQPHGIRPFGMRAMMSLRLDKFFGAWSREYSPDYTAAETGLDRFIHFGKNTAFIG 703 Query: 279 SEALKQVVAQGGPKRKLVGLEMIDRGIARDGYRVLNDTQQAVGYVTSGSPAPFLKKNIAL 338 A + A P R+L E+ Y ++ + VG+ TSG A F K+IAL Sbjct: 704 RNAAEAERATP-PARQLCAFEVAATDADVVAYEPISLDGEVVGFCTSGGYAHFTGKSIAL 762 Query: 339 AYVPTELATLDREVFVEIRNNPVKARIVPTPFY 371 +VP E+A E +EI + A ++ TP + Sbjct: 763 GFVPREMAQDGLEASIEILGDHCPATLITTPLF 795 Lambda K H 0.320 0.136 0.407 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: 718 Number of extensions: 41 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 378 Length of database: 804 Length adjustment: 36 Effective length of query: 342 Effective length of database: 768 Effective search space: 262656 Effective search space used: 262656 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 (21.8 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