Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate H281DRAFT_06542 H281DRAFT_06542 4-methylaminobutanoate oxidase (formaldehyde-forming)
Query= curated2:B8D1D7 (357 letters) >FitnessBrowser__Burk376:H281DRAFT_06542 Length = 826 Score = 153 bits (386), Expect = 2e-41 Identities = 111/353 (31%), Positives = 179/353 (50%), Gaps = 29/353 (8%) Query: 2 KKTPLFEIHKELGARLIEFHGWSM-----PVQYTSIIE--------------EHKAVRNQ 42 +++PL+ + +E GA GW P + + I+ EH+A R + Sbjct: 431 RRSPLYALLREDGACFGSKMGWERANFFAPTRDEARIDYAFGQQNWLPLSGAEHRACRER 490 Query: 43 CGLFDVSHMGEILVEGPGALESLQKIVTNNVARLKKGQVLYTPMCKDDGGIIDDLLVYCL 102 LFD++ + LV+G A LQ +V N+V + G +YT M + G D + L Sbjct: 491 VALFDMTSFSKFLVKGRDAQSVLQNLVANDVD-VPPGTTVYTGMLNERGNYESDFTLTRL 549 Query: 103 GQDKYLMVVNASNIEKDFNWVRDNSNQRTE---VVNESDNYALLALQGPNSKKILEKVSS 159 D+YL+V + +DF+ + D + R + +V+ + YA+LA+ GP S+++L+ VS Sbjct: 550 AADQYLLVTGTAQTTRDFDMI-DKAIPRDKHCVLVDVTSQYAVLAVMGPRSRELLQSVSK 608 Query: 160 VNL--DSLKFYNFTTGTLKGAEVLISRTGYTGELGYELYLSPDKAVEVWQALMEAGSDLG 217 + +S F + A V +R Y GELG+ELY+ + AV V++ L EAG G Sbjct: 609 ADWRNESFAFGQSREVDIGYATVRATRLTYVGELGWELYVPVEFAVGVYEILHEAGKAFG 668 Query: 218 LIPAGLGARDTLRLEKGYCLYGNDIDENTHPLEAGLGWTVKFD-KASFIGKRALLKYKEE 276 L+ AG A D+LR+EKGY +G ++ +T+P EA L + K D F G+ AL + + + Sbjct: 669 LVNAGYYAIDSLRIEKGYRAWGRELTPDTNPFEAALAFACKLDTDIPFRGRDALAELRGK 728 Query: 277 GLSRKLVGFKLKGRG--IPRHGYPIKDNGDQIGVVTSGSMSPTLSEGIGMGYV 327 L R++V G + G I +G +G V+S + TL + MGYV Sbjct: 729 PLRRRMVVLTADGAADRMLWGGEAILRDGKPVGFVSSAAFGHTLGCPVAMGYV 781 Lambda K H 0.317 0.138 0.404 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: 30 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: 357 Length of database: 826 Length adjustment: 35 Effective length of query: 322 Effective length of database: 791 Effective search space: 254702 Effective search space used: 254702 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 (21.6 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