Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate GFF3260 PGA1_c33110 sarcosine dehydrogenase
Query= curated2:B8D1D7 (357 letters) >FitnessBrowser__Phaeo:GFF3260 Length = 816 Score = 179 bits (453), Expect = 3e-49 Identities = 114/316 (36%), Positives = 174/316 (55%), Gaps = 15/316 (4%) Query: 21 HGWSMPVQYTSIIEEHKAVRNQCGLFDVSHMGEILVEGPGALESLQKIVTNNVARLKKGQ 80 + W + + EH+AVR G++D+S G+I VEGP A L I N++ + G+ Sbjct: 464 YSWKRQNWFENSAAEHRAVRENIGMYDMSSFGKIRVEGPDAEIFLNYICGANLS-VPAGK 522 Query: 81 VLYTPMCKDDGGIIDDLLVYCLGQDKYLMVVNASNIEKDFNWV-RDNSNQRTEVVNESDN 139 ++YT GGI D+ V L + YL+V A D W+ R + R + + + Sbjct: 523 IVYTQFLNARGGIEADVTVTRLSETAYLVVTPAVTRLTDQTWMMRHVGDHRVVITDVTAG 582 Query: 140 YALLALQGPNSKKILEKVSSVNLDSLKFYNFTT--GTLKGAEV-----LISRTGYTGELG 192 +LA+ GPN++K+L+KVS + F N GT + E+ + R Y GELG Sbjct: 583 EGVLAVMGPNARKLLQKVSPND-----FSNAVNPFGTAQEIELGMGLARVHRVTYVGELG 637 Query: 193 YELYLSPDKAVEVWQALMEAGSDLGLIPAGLGARDTLRLEKGYCLYGNDIDENTHPLEAG 252 +E+Y+S D A ++ L EAG D+GL G+ D+ R+EKG+ +G+DI + ++AG Sbjct: 638 WEIYVSADMAGHAFETLHEAGQDMGLKLCGMHMMDSCRIEKGFRHFGHDITCEDNVIDAG 697 Query: 253 LGWTVKFDKASFIGKRALLKYKEEGLSRKLVGFKL-KGRGIPRHGYPIKDNGDQIGVVTS 311 LG+ VK DKA FIGK A+L KE G +++ FKL + + H PI +G +G ++S Sbjct: 698 LGFAVKTDKADFIGKSAVLARKETGPMNRMLQFKLTESEPLLFHNEPIIRDGKYVGYLSS 757 Query: 312 GSMSPTLSEGIGMGYV 327 G+ TL+ IGMGYV Sbjct: 758 GNYGHTLAAAIGMGYV 773 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: 665 Number of extensions: 40 Number of successful extensions: 6 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: 816 Length adjustment: 35 Effective length of query: 322 Effective length of database: 781 Effective search space: 251482 Effective search space used: 251482 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 Apr 09 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