Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate GFF2307 PGA1_c23390 putative sarcosine dehydrogenase
Query= curated2:P54261 (372 letters) >FitnessBrowser__Phaeo:GFF2307 Length = 807 Score = 171 bits (432), Expect = 9e-47 Identities = 125/385 (32%), Positives = 189/385 (49%), Gaps = 38/385 (9%) Query: 10 TPLYNLITEQTTKLTTFGGWEMPVQFAG-------------------LKQEHQAVREKVG 50 +PL++ + + + GWE P+ FA +QEH AVR V Sbjct: 423 SPLHDRLKQHGAVFGSKNGWERPLWFAPEGVEPVDQLDFLNPGWKVFAEQEHSAVRNGVV 482 Query: 51 MFDISHMGKFVLTGQKVLAALQSLVPSDLDRLTPGKAQYTVLLNAQGGIIDDIIVYDQGK 110 + D S KF L G LAA+Q+L S++D+ G YT L N QGG DI V G+ Sbjct: 483 LIDQSSFSKFELIGPGALAAIQNLAVSNMDK-PDGAVIYTQLCNMQGGTEADITVTRLGR 541 Query: 111 NPEGQERVTLIVNAATTVKDKQWLLEHLPEEIDFQ--DLSREKVLIALQGPEALTILQPL 168 + ++ A V D W+ HLPE+ Q +++ + +I L GP++ +LQ + Sbjct: 542 -----DHFYIVTGAGFGVHDADWIRRHLPEDGSAQLIEMTSARAVINLCGPKSREVLQAV 596 Query: 169 VDQNLGELPAFGHLEAEFLREKAFI---ARTGYTGEDGFEIMVSPE----VGKQLWQTFG 221 ++++ AF A+ + A AR GYTGE G+E+ V E V LWQ Sbjct: 597 SEEDVSNR-AFPFATAQDITLGAATVRAARIGYTGELGWELHVPTEFALHVYDLLWQAGQ 655 Query: 222 SKGVTPCGLGARDTLRLEAGMGLYGQDMNDETTPLEAGLGWLVHLDSKGDFIGRAVLTEQ 281 G+ G A ++LRLE G + D+ + +P+EAGL VHL SK DF+GRA+L Q Sbjct: 656 EHGIRDIGYRAIESLRLEKGYVYWSADITPDYSPVEAGLAGRVHLKSKEDFLGRAILDRQ 715 Query: 282 KANGVEKRLVGLEMLAKQIARHDYPILHNGEIMGIVTSGTLSPTLQKAIALGYVPTELAK 341 K G ++L + + ILH G+ + + +SG PT +K I GY+PT L Sbjct: 716 KREGTSQQLCTFTVDERLPMTGGETILHKGKAVSLASSGGYGPTAEKTIVYGYLPTAL-- 773 Query: 342 VGQ-ELEVEVRGKTYGIKVVKKLFY 365 VG+ + E+E+ G+ ++ V Y Sbjct: 774 VGERDFELELFGRRQALRQVDGPLY 798 Lambda K H 0.318 0.137 0.397 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: 796 Number of extensions: 48 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: 372 Length of database: 807 Length adjustment: 35 Effective length of query: 337 Effective length of database: 772 Effective search space: 260164 Effective search space used: 260164 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 (21.7 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