Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate WP_086510494.1 BZY95_RS13790 sarcosine oxidase subunit alpha family protein
Query= curated2:O86567 (372 letters) >NCBI__GCF_002151265.1:WP_086510494.1 Length = 1016 Score = 149 bits (375), Expect = 4e-40 Identities = 107/356 (30%), Positives = 163/356 (45%), Gaps = 27/356 (7%) Query: 7 RRTALDATHRALGATMTDFAGWDMP------------LRYGSEREEHVAVRTRAGLFDLS 54 R TAL H GA D W P + + E AVR + G+ D S Sbjct: 623 RYTALHQWHVENGAEFEDVGQWKRPWYFPKVVNGKKETMFDAVARECRAVREKVGILDAS 682 Query: 55 HMGEITVTGPQAAELLNFALVGNIGTVKPGRARYTMICREDGGILDDLIVYRLEEAEYMV 114 +G+I + GP A E L + G+ RY ++C++DG + DD + L + +++ Sbjct: 683 TLGKIDIQGPDAREFLGRVYTNKWEKLAVGKCRYGLMCKDDGMVTDDGVTSCLADNHFLM 742 Query: 115 VANASNAQVVLDALT----ERAAGFDAEVRDDRDAYALLAVQGPESPGILASLTDADLDG 170 A VL+ L + D +A + + GPE+ +LA +TD DLD Sbjct: 743 TTTTGGAAAVLEWLELWHQTEWPELNVTFTSVTDHWATMTITGPEARNLLAEITDIDLDR 802 Query: 171 --LKYYAGLPGTVAGVPALIARTGYTGEDGFELFVKPEHAVGLWQALTGAGEAAGLIPCG 228 K+ G VAGVPA + R +TGE +E+ V+ +A+ +W+ L GE GL P G Sbjct: 803 DTFKFMDWREGKVAGVPARVFRISFTGELTYEINVQANYAMHVWKTLFSHGEKYGLTPYG 862 Query: 229 LSCRDTLRLEAGMPLYGNELSTALTPFDAGLGRVVKFEKEGDFVGRAALTEAAERAASRP 288 LR E G + G + ++TP D G+ V ++K ++G+ ALT + R R Sbjct: 863 TETMHVLRAEKGFIIVGQDTDGSVTPEDLGMQWCVGYDKPYSWIGKRALTRSDTRRTDR- 921 Query: 289 PRVLVGLVAEGRRVP-RSGYRVVAGGE------VIGEVTSGAPSPTLGRPIAMAYV 337 + LVGL + +V G ++V + + G VTS SPTL A+A V Sbjct: 922 -KQLVGLKPKDPKVVLEEGAQIVFDPKHAIPMPMAGHVTSSYYSPTLDSGFALAVV 976 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: 905 Number of extensions: 37 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: 1016 Length adjustment: 37 Effective length of query: 335 Effective length of database: 979 Effective search space: 327965 Effective search space used: 327965 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