Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate SMa2145 SMa2145 glycine cleavage system protein T
Query= curated2:Q8DKV6 (366 letters) >FitnessBrowser__Smeli:SMa2145 Length = 418 Score = 158 bits (400), Expect = 2e-43 Identities = 118/390 (30%), Positives = 182/390 (46%), Gaps = 43/390 (11%) Query: 15 PLHQGARFTPFGDWEMPLQYSSILQEHQAVRQQVGMFDISHMGKLVLRGEGVLGALQTLV 74 PL+Q A + + + YS ++ E A+R V M D+S + K V+ G + L+ Sbjct: 31 PLNQNALWMRWDRNMVVDAYSDMVAELSAIRTAVAMGDMSPLSKYVIAGPDAEAMMDRLI 90 Query: 75 PTNLSQLQPGQAKYTVLLNEAGGIVDDVILYMGDGQVRCIVNAATTAKDWAWFQKYLPAS 134 P ++ +LQ GQ Y +E G +V D +++ D + +A W W Q Sbjct: 91 PRDIRKLQVGQIYYAPWCDENGYVVGDGLVFRMDENTFRV--SADPGFTW-WRQHAEGLD 147 Query: 135 IEVIDESASQVLIALQGPAATATLSPLCDRPLGEIKTYRHAPVNLLGQPAWIARTGYTGE 194 ++V D + + ++ LQGP + L + E+ R A V + G+ I R G+TGE Sbjct: 148 LQVTDITDTYGILTLQGPRSREVLEAATEAGFQELPFSRLAVVTIAGRQVEILRQGFTGE 207 Query: 195 DGWEILVPAELGQQLWQTLLAAG----VTPCGLGARDTLRLEAAMLLYGQDMDE------ 244 G+E+ V AE G +W + AAG + P G A D RLEA +L+ G D Sbjct: 208 HGYELWVKAEDGPTVWDAVEAAGRPFSIRPAGAWALDVARLEAGLLIVGYDYTSAGPDHG 267 Query: 245 ----------QTTPLEAGLDGLIDWQKPDFVGRAALLAQKQQGIERQLVGLELLGKGIAR 294 + +P + GL L+D++K DF+GR AL + G RQLVGLE+ K IA Sbjct: 268 GAGIQASGKFRASPFDLGLGRLVDFKKSDFIGRTALERLSKYGQHRQLVGLEIDWKQIAG 327 Query: 295 HG----------------YPIYAGAQAVGEVTSGTLSPTLGKAIALGYVFPEFAHIGREL 338 G P++ G+ +G +S SPTL K I G++ F IG ++ Sbjct: 328 TGLESEEPGNLRRVRWYPVPVFGGSVEIGHASSVAWSPTLRKLIGFGHLQQAFGEIGTQV 387 Query: 339 AVQVRD----RWVPAVVVPRPFYRRPRSTA 364 ++ D R V A VV PF+ R+ + Sbjct: 388 TLRWEDDGTTRDVAARVVALPFHSLRRTAS 417 Lambda K H 0.320 0.137 0.419 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: 432 Number of extensions: 26 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: 366 Length of database: 418 Length adjustment: 31 Effective length of query: 335 Effective length of database: 387 Effective search space: 129645 Effective search space used: 129645 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: 50 (23.9 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