Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate 3608872 Dshi_2264 sarcosine oxidase, alpha subunit family (RefSeq)
Query= curated2:Q6A9R6 (371 letters) >FitnessBrowser__Dino:3608872 Length = 980 Score = 108 bits (269), Expect = 8e-28 Identities = 105/345 (30%), Positives = 159/345 (46%), Gaps = 29/345 (8%) Query: 42 VRKNAGIFDLSHMGEIRISGPDSGAALDYALAGKLSAVAEGRAKYSLLLTDEGGVVDDLV 101 VR G+ D+S +G+I + GPD+GA LD A S + GR +Y ++L ++G V+DD Sbjct: 638 VRSAVGVCDVSTLGKIELQGPDAGAFLDLVYANTFSTLKPGRVRYGVMLREDGHVMDDGT 697 Query: 102 TYHLPDGDYLVVAN--AANAETDLAEFTKRC--ARFDVTVTDESAQTALVAVQGPTAVKI 157 T L G Y++ AA+ EF ++C V T + A AV GP A + Sbjct: 698 TACLGPGHYVMTTTTVAAHKVMQHLEFVQQCLVPTMRVRFTSVTENWAQFAVAGPQARAL 757 Query: 158 VLAALQKANTTLDSDEVRDVK--YYRCLTGELDGFPVLVARTGYTGEDGYELYVPAKAAA 215 + N LD+ VR+ + C L G + R ++GE YE+ +PA+ A Sbjct: 758 L-------NDLLDA-PVRNANFPFMACGAVRLGGVGGRLFRISFSGEHAYEVAIPARYGA 809 Query: 216 HLW-QLLMDAGGEDLTPCGLACRDTLRLEAGMPLYGHELGTDIHPSQAGLGRVVNFKKEG 274 L+ QL+ A G+ + LR+E G + E+ + GLGR+V+ KK Sbjct: 810 ALFEQLVARAEAMGGGAYGMEALNVLRIEKGFVTHA-EIHGRVTADDVGLGRMVSAKK-- 866 Query: 275 DFVGRCALENRD-TTADR-VLVGLTG-EGRRAGRAGYAVVNEDKTV------GAITSGIL 325 D +G+ A + T DR LVGL +GR A AG + G +TS Sbjct: 867 DCIGKTASQRPGLTDPDREQLVGLRPCDGRTALLAGAHLFEPGAEAVRVTDQGYVTSVCF 926 Query: 326 SPTLGHPIAMAFVDPDVAKIGTSLSV--DVRGKALNTTVVELPFY 368 SPTL PI + F+ A+ G + + +RG V + F+ Sbjct: 927 SPTLQTPIGLGFLRRGRARHGQRVMMIDHLRGVTTECEVTDPVFF 971 Lambda K H 0.318 0.135 0.394 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: 811 Number of extensions: 42 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 371 Length of database: 980 Length adjustment: 37 Effective length of query: 334 Effective length of database: 943 Effective search space: 314962 Effective search space used: 314962 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: 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