Align Probable glycine dehydrogenase (decarboxylating) subunit 2; EC 1.4.4.2; Glycine cleavage system P-protein subunit 2; Glycine decarboxylase subunit 2; Glycine dehydrogenase (aminomethyl-transferring) subunit 2 (uncharacterized)
to candidate WP_011383212.1 AMB_RS03940 glycine dehydrogenase (aminomethyl-transferring)
Query= curated2:Q9A354 (524 letters) >NCBI__GCF_000009985.1:WP_011383212.1 Length = 499 Score = 665 bits (1715), Expect = 0.0 Identities = 331/496 (66%), Positives = 379/496 (76%), Gaps = 3/496 (0%) Query: 22 TLTGARGLLQDEALIFELDGWNKTGVDLPPVTAAPSSDLNGLLRDAPIGLPGLSEPETVR 81 T++G R L +E LIFEL VDLP L R + LP LSEP+ VR Sbjct: 6 TISGNRALQIEEKLIFELGNPGSVAVDLPEPAPFDLERLGDAPRRGRVALPDLSEPQVVR 65 Query: 82 HYVRLSQKNHAIDLALYPLGSCTMKHNPRLNEKMARLPGFSDIHPLQPQSTVQGALELMD 141 HY RLSQKN+ ID YPLGSCTMKHNPRL+EK+ARLPG +D+HPLQPQ TVQGALE++D Sbjct: 66 HYTRLSQKNYGIDTGFYPLGSCTMKHNPRLSEKVARLPGLADLHPLQPQKTVQGALEVID 125 Query: 142 RLAHWLKTLTGMPAVALTPKAGAHGELCGLLAIRAAHEAAGNGHRKTVLAPTSAHGTNPA 201 LAHWLK LTGMPAVA++P AGAHGE CGL+AIR+AHE G GHRK VL P SAHGTNPA Sbjct: 126 TLAHWLKALTGMPAVAMSPAAGAHGEWCGLMAIRSAHEDKGEGHRKRVLVPESAHGTNPA 185 Query: 202 TAAFVGYTVVEIAQTEDGRVDLADLESKLGDHVAAIMVTNPNTCGLFERDVVEIARLTHA 261 +AA GYTV I E+GRVDLA L++KLG VA +M+TNPNTCGLFE ++VEIA H Sbjct: 186 SAAMCGYTVDPIPALENGRVDLAALKAKLGPDVACLMLTNPNTCGLFETEIVEIAAAVHG 245 Query: 262 AGAYFYCDGANFNAIVGRVRPGDLGVDAMHINLHKTFSTPHGGGGPGAGPVVLSEALAPF 321 AGAYFYCDGANFNAIVGRV+ DLG+DAMHINLHKTF+TPHGGGGPGAGP VLS ALA F Sbjct: 246 AGAYFYCDGANFNAIVGRVKIADLGIDAMHINLHKTFATPHGGGGPGAGPTVLSAALAAF 305 Query: 322 APTPWLTHGDNGFELAEHAGDDDAKTAFGRMSAFHGQMGMYVRAYAYMLSHGADGLRQVA 381 P P++ HG +G EL E G D FGR+ FHGQ G++VRA AY+ S G+DGLRQ + Sbjct: 306 VPVPYVVHGASGLELVE--GKRDGAKPFGRVKGFHGQFGVFVRALAYIQSMGSDGLRQAS 363 Query: 382 EDAVLNANYIKAQLKDVMSPAFPEGPCMHEALFDDSWLEGTGVTTLDFAKAMIDEGFHPM 441 DAVLNANY+ A LKD +S +F +GPCMHEALFDD +L+ TGVTTLDFAKAMIDEG+HPM Sbjct: 364 SDAVLNANYLLASLKDELSASF-DGPCMHEALFDDRFLKDTGVTTLDFAKAMIDEGYHPM 422 Query: 442 TMYFPLVVHGAMLIEPTETESKHELDRFIAALRALAGAAKAGDTERFKGAPFHAPLRRLD 501 TMYFPLVVHGA+L+EPTETESK LD+FIA ++ LA AKAG E FK AP P RRLD Sbjct: 423 TMYFPLVVHGALLMEPTETESKDTLDQFIAVVKGLAAKAKAGGVEDFKAAPRLTPRRRLD 482 Query: 502 ETQAARKPRLRWKPVA 517 ET AAR P LRWK A Sbjct: 483 ETLAARSPVLRWKTAA 498 Lambda K H 0.318 0.135 0.411 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: 847 Number of extensions: 29 Number of successful extensions: 3 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: 524 Length of database: 499 Length adjustment: 35 Effective length of query: 489 Effective length of database: 464 Effective search space: 226896 Effective search space used: 226896 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: 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