Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate SMc04148 SMc04148 aminomethyltransferase
Query= curated2:Q67N36 (375 letters) >FitnessBrowser__Smeli:SMc04148 Length = 789 Score = 201 bits (510), Expect = 8e-56 Identities = 126/339 (37%), Positives = 195/339 (57%), Gaps = 17/339 (5%) Query: 24 FGGWEMPVQYSSV--IEEHRAVREAAGLFDVSHMGEFEVRGPQALDLIQLVSTNDAAKLA 81 + G+ +P ++SS +EE+ A RE A + D+S + +FEV GP A +L+Q T D KL+ Sbjct: 429 YRGYWLPNRFSSAGPVEEYWACRERAAVIDLSPLRKFEVTGPDAEELLQYCLTRDVRKLS 488 Query: 82 VGRVQYALMCYENGTVVDDILIYRLDEHRY-WLVVNAGNTQKDWEWINTARERAGLHNLE 140 G+V Y+ MCYE+G ++DD ++RL + + W+ G W+ E+ G Sbjct: 489 TGQVVYSAMCYEHGGMIDDGTLFRLGDKNFRWI----GGDDYSGIWLREQAEKKGFRAW- 543 Query: 141 LIDRSAEIALLALQGPKAEEILQPLATGV----VLSQLE--PFSLAKNVTVSGVPTLVLS 194 + + ++ +A+QGPK+ +IL+ + + +LE F++ + G P +V+S Sbjct: 544 VRSSTDQMHNIAVQGPKSRDILKEIVWTAPRQPTIGELEWFRFAVGRIGGFEGAP-IVVS 602 Query: 195 RTGYTGEDGFEIYVKAEDVAALWEALLEAGDEQGLLPCGLGARDTLRFEAKLPLYGHEIS 254 RTGYTGE G+EI+ +D +++A+ AG+ GL P GL A D +R EA L ++ Sbjct: 603 RTGYTGELGYEIFCHPKDALTVFDAVWRAGEPHGLRPMGLEALDMVRIEAGLIFAHYDFD 662 Query: 255 DQHNPLEAGLGFAVKLK-KGVDFIGRDALARIKEQGPTRKLVGIEMIDRGVPRQGYPVAV 313 DQ +P EAG+GF V LK K DFIGR+AL R KE P +VG+++ G V V Sbjct: 663 DQTDPFEAGIGFTVPLKSKHDDFIGREALIRRKE-NPRHLMVGLDIQANEAVGHGDCVHV 721 Query: 314 GGEVVGEVTTGSFSPTLEKNIALAYVPVAHSAVGTEVEV 352 G +G +T+ + SP L K IALA + V H+ VGT+VE+ Sbjct: 722 GRAQIGVITSATRSPVLGKTIALARIDVTHATVGTQVEI 760 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: 681 Number of extensions: 34 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: 375 Length of database: 789 Length adjustment: 35 Effective length of query: 340 Effective length of database: 754 Effective search space: 256360 Effective search space used: 256360 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: 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