Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate WP_011840959.1 RSPH17029_RS06825 sarcosine oxidase subunit alpha family protein
Query= curated2:Q67N36 (375 letters) >NCBI__GCF_000015985.1:WP_011840959.1 Length = 993 Score = 171 bits (433), Expect = 8e-47 Identities = 129/393 (32%), Positives = 185/393 (47%), Gaps = 36/393 (9%) Query: 3 ESLKRTPLYELHLKLGARMVPFGGWEMPVQYSSVIEEH--------RAVREAAGLFDVSH 54 + L+RTP+++ H GA P G W P YS E H R GL D S Sbjct: 602 QPLRRTPMHDWHEANGAYWEPVGLWRRPYCYSRPGESHGDAVAREVTNARTKLGLLDAST 661 Query: 55 MGEFEVRGPQALDLIQLVSTNDAAKLAVGRVQYALMCYENGTVVDDILIYRLDEHRYWLV 114 +G+ V+GP A + ++ TN + L VGR +Y LMC ENG ++DD ++ RL E + Sbjct: 662 LGKILVKGPDAGRFLDMLYTNVMSSLPVGRCRYGLMCNENGFLMDDGVVVRLSEDSWLCH 721 Query: 115 VNAGNTQK------DW---EWINTARERAGLHNLELIDRSAEIALLALQGPKAEEILQPL 165 +G + DW EW + A L + + A +A+ GP A +L+ L Sbjct: 722 TTSGGADRIHAHMEDWLQCEWWDWQVYTANL--------TEQFAQVAIVGPNARLLLEKL 773 Query: 166 ATGVVLSQLEPFSLAKNVTVSGVPTLVLSRTGYTGEDGFEIYVKAEDVAALWEALLEAGD 225 V + PF T++G+P V R ++GE +E+ V A A W+A LEAG Sbjct: 774 GGMDVSKEALPFMHWAEGTLAGIPARVF-RISFSGELSYEVAVPAGQGLAFWQACLEAGA 832 Query: 226 EQGLLPCGLGARDTLRFEAKLPLYGHEISDQHNPLEAGLGFAVKLKKGVDFIGRDALARI 285 E GL+P G A +R E + G E P + LG+A+ KK DFIG+ + R Sbjct: 833 EFGLMPYGTEALHVMRAEKGFIMIGDETDGTVVPQDLNLGWAIS-KKKADFIGKRGMERT 891 Query: 286 KEQGPTR-KLVGIEMIDRGVPRQGYPVAVGG-------EVVGEVTTGSFSPTLEKNIALA 337 P R KLVG+E +D V G G G VT+ +SPTL+K IA+ Sbjct: 892 FLSSPDRWKLVGLETLDGSVLPDGAIAPAAGSNGNGQRNTQGRVTSTYWSPTLKKGIAMG 951 Query: 338 YVPVAHSAVGTEVEV-IIRGRALKARVVETPFY 369 V +G +E I G ++AR+V+ FY Sbjct: 952 LVHRGTDRMGEVIEFPKIWGGVVQARIVDPVFY 984 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: 839 Number of extensions: 37 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: 375 Length of database: 993 Length adjustment: 37 Effective length of query: 338 Effective length of database: 956 Effective search space: 323128 Effective search space used: 323128 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 Apr 10 2024. 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