Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate SMc01662 SMc01662 oxidoreductase
Query= curated2:A4J2F6 (364 letters) >FitnessBrowser__Smeli:SMc01662 Length = 815 Score = 169 bits (427), Expect = 3e-46 Identities = 114/344 (33%), Positives = 176/344 (51%), Gaps = 11/344 (3%) Query: 26 WLMPVQYEGIIAEHQAVRSAAGLFDVSHMGEIQISGPTAREFVQRLVTNDISRLKPGCAI 85 W +E EH AVRS GLFD++ G+I++ G A+ F+QRL N+++ + PG + Sbjct: 465 WKRQNWFENQREEHLAVRSGVGLFDMTSFGKIRVEGRDAQAFLQRLCANEMN-VDPGRVV 523 Query: 86 YSPMCNPQGGTVDDLLVYQLEDQQYLLVVNASNTDKDFHWIVSQ-QVPGVEIQNVSEVTC 144 Y+ M N +GG DL V +L + LVV + +D W+ + V I +V+ Sbjct: 524 YTQMLNARGGIESDLTVTRLSQTAFFLVVPGATLQRDLAWLRKHVRDEFVVITDVTAAES 583 Query: 145 QLALQGPQAEKILQRLTAVDLSHIKSFCFVYGAVE---GIHCLISRTGYTGEAGFELYFP 201 L + GP+A +++Q+++ D S+ +E G+ R Y GE G+ELY Sbjct: 584 VLCVMGPRARELMQKVSPNDFSNEAHPFATAREIEIGMGL-ARAHRVTYVGELGWELYVS 642 Query: 202 ASHAERVWQAIMATGATDGLRPVGLGARDTLRFEACLALYGHELTDDISPLMAGLGWTVK 261 A V++ + GA GL+ GL D+ R E +GH++TD+ L AGLG+ VK Sbjct: 643 TDQAAHVFETLELAGADVGLKLCGLHTLDSCRIEKAFRHFGHDITDEDHVLEAGLGFAVK 702 Query: 262 FNKPEFVGKEPLLKQKEAGTTYQLVGLEMID-RGIPRQGYAIFKEGQEVGWITSGTFAPT 320 K EF+G+E +L +++ G + +LV + D + AI ++G+ VG ITSG + Sbjct: 703 PGKGEFIGREAVLAKRDNGLSRRLVQFRLSDPEPLLFHNEAIVRDGEIVGTITSGNYGHH 762 Query: 321 LGKNMGLGYVEI---PFADV-GKELNIMVRNKPLKARIVKKPFY 360 LG +GLGYV ADV I + +KA KP Y Sbjct: 763 LGGAIGLGYVACKGESDADVLASAYEIEIAGTRVKAEASLKPMY 806 Lambda K H 0.321 0.138 0.418 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: 686 Number of extensions: 50 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: 364 Length of database: 815 Length adjustment: 35 Effective length of query: 329 Effective length of database: 780 Effective search space: 256620 Effective search space used: 256620 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: 52 (24.6 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