Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate 3609583 Dshi_2967 FAD dependent oxidoreductase (RefSeq)
Query= curated2:Q24TH3 (365 letters) >FitnessBrowser__Dino:3609583 Length = 831 Score = 138 bits (348), Expect = 5e-37 Identities = 111/378 (29%), Positives = 174/378 (46%), Gaps = 44/378 (11%) Query: 4 LKRTPLYEQHRRAGAKLIDFGGWEMPVQYAGVIE-----------------------EHK 40 L+ TP Y++ + GA+ GWE P Y G ++ E + Sbjct: 433 LRTTPAYDRQKALGAQFGQVNGWERP-NYYGPLDAPDNFDHDARSFRRGGWWDYARAEAE 491 Query: 41 AVRSKAGLFDVSHMGEVELKGKDSLAFLQYLLTNDVSRIQDNQIQYSPMCTSAGGVVDDL 100 AVRS AGL D + + + G + AFL + TN + R+ + Y+ T AG + Sbjct: 492 AVRSTAGLIDATAFAKHRVSGPGATAFLDWFTTNTLPRVGRINLTYA--LTGAGTTHTEY 549 Query: 101 LVYRYSREHFLLVVNAA--NTDKDF---AWMQAQAEGFEISLENRSGDFAQLALQGPWAE 155 + R + + L+ A D+DF A + I+L++ + AL GP A Sbjct: 550 TILRTGEDDYTLISAGAWHAYDQDFLTKAIEDTEPRFGRITLQDTTTQTGVFALAGPKAR 609 Query: 156 KILQKLT-----SMDLAQINYYWFKHGEVDGVLCLIS--RTGYTGEDGFEIYLPPEHAPR 208 IL+ L L+ + W E++ +C + R YTG G+E++ P E Sbjct: 610 DILKALIRDPDPETALSNKRFPWLGTREIELGMCPLRAVRVAYTGALGWELHHPIEMQTY 669 Query: 209 MWERILEVGGSEGVQPIGLGARDTLRFEARLPLYGNELGPDITPLEAGLGFFVKLEKDNF 268 +W++++ VG + G++P+G A++ LR E +G ELG D TPLEAGL FV L KD F Sbjct: 670 LWDQLMAVGAAHGLKPVGARAQNWLRQEKSYRAFGTELGRDATPLEAGLDRFVDLSKD-F 728 Query: 269 IGKEALSAQKEKGVPRKLVGL--EMIERGIARSHYPLQKEGKEIGFITSGSFSPTLNKNI 326 GK +A E G+ + V L + + L +G +TSG +S K+I Sbjct: 729 HGK---AAMVETGIRSRCVTLLIDGPDDADPWGREALYAGDTRVGRLTSGGYSVAFGKSI 785 Query: 327 ALGLIPPEYAQIGETLDV 344 A+G + P++A G L V Sbjct: 786 AMGYVTPDHAAPGTKLKV 803 Lambda K H 0.319 0.139 0.412 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: 721 Number of extensions: 30 Number of successful extensions: 4 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: 365 Length of database: 831 Length adjustment: 36 Effective length of query: 329 Effective length of database: 795 Effective search space: 261555 Effective search space used: 261555 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: 53 (25.0 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