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 CCNA_03462 CCNA_03462 glycine cleavage system protein P, C-terminal domain
Query= curated2:Q9A354 (524 letters) >FitnessBrowser__Caulo:CCNA_03462 Length = 526 Score = 1068 bits (2763), Expect = 0.0 Identities = 524/524 (100%), Positives = 524/524 (100%) Query: 1 MNNVGRPTRPEAANDAANGHETLTGARGLLQDEALIFELDGWNKTGVDLPPVTAAPSSDL 60 MNNVGRPTRPEAANDAANGHETLTGARGLLQDEALIFELDGWNKTGVDLPPVTAAPSSDL Sbjct: 3 MNNVGRPTRPEAANDAANGHETLTGARGLLQDEALIFELDGWNKTGVDLPPVTAAPSSDL 62 Query: 61 NGLLRDAPIGLPGLSEPETVRHYVRLSQKNHAIDLALYPLGSCTMKHNPRLNEKMARLPG 120 NGLLRDAPIGLPGLSEPETVRHYVRLSQKNHAIDLALYPLGSCTMKHNPRLNEKMARLPG Sbjct: 63 NGLLRDAPIGLPGLSEPETVRHYVRLSQKNHAIDLALYPLGSCTMKHNPRLNEKMARLPG 122 Query: 121 FSDIHPLQPQSTVQGALELMDRLAHWLKTLTGMPAVALTPKAGAHGELCGLLAIRAAHEA 180 FSDIHPLQPQSTVQGALELMDRLAHWLKTLTGMPAVALTPKAGAHGELCGLLAIRAAHEA Sbjct: 123 FSDIHPLQPQSTVQGALELMDRLAHWLKTLTGMPAVALTPKAGAHGELCGLLAIRAAHEA 182 Query: 181 AGNGHRKTVLAPTSAHGTNPATAAFVGYTVVEIAQTEDGRVDLADLESKLGDHVAAIMVT 240 AGNGHRKTVLAPTSAHGTNPATAAFVGYTVVEIAQTEDGRVDLADLESKLGDHVAAIMVT Sbjct: 183 AGNGHRKTVLAPTSAHGTNPATAAFVGYTVVEIAQTEDGRVDLADLESKLGDHVAAIMVT 242 Query: 241 NPNTCGLFERDVVEIARLTHAAGAYFYCDGANFNAIVGRVRPGDLGVDAMHINLHKTFST 300 NPNTCGLFERDVVEIARLTHAAGAYFYCDGANFNAIVGRVRPGDLGVDAMHINLHKTFST Sbjct: 243 NPNTCGLFERDVVEIARLTHAAGAYFYCDGANFNAIVGRVRPGDLGVDAMHINLHKTFST 302 Query: 301 PHGGGGPGAGPVVLSEALAPFAPTPWLTHGDNGFELAEHAGDDDAKTAFGRMSAFHGQMG 360 PHGGGGPGAGPVVLSEALAPFAPTPWLTHGDNGFELAEHAGDDDAKTAFGRMSAFHGQMG Sbjct: 303 PHGGGGPGAGPVVLSEALAPFAPTPWLTHGDNGFELAEHAGDDDAKTAFGRMSAFHGQMG 362 Query: 361 MYVRAYAYMLSHGADGLRQVAEDAVLNANYIKAQLKDVMSPAFPEGPCMHEALFDDSWLE 420 MYVRAYAYMLSHGADGLRQVAEDAVLNANYIKAQLKDVMSPAFPEGPCMHEALFDDSWLE Sbjct: 363 MYVRAYAYMLSHGADGLRQVAEDAVLNANYIKAQLKDVMSPAFPEGPCMHEALFDDSWLE 422 Query: 421 GTGVTTLDFAKAMIDEGFHPMTMYFPLVVHGAMLIEPTETESKHELDRFIAALRALAGAA 480 GTGVTTLDFAKAMIDEGFHPMTMYFPLVVHGAMLIEPTETESKHELDRFIAALRALAGAA Sbjct: 423 GTGVTTLDFAKAMIDEGFHPMTMYFPLVVHGAMLIEPTETESKHELDRFIAALRALAGAA 482 Query: 481 KAGDTERFKGAPFHAPLRRLDETQAARKPRLRWKPVAAAPLAAE 524 KAGDTERFKGAPFHAPLRRLDETQAARKPRLRWKPVAAAPLAAE Sbjct: 483 KAGDTERFKGAPFHAPLRRLDETQAARKPRLRWKPVAAAPLAAE 526 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: 1206 Number of extensions: 36 Number of successful extensions: 1 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: 526 Length adjustment: 35 Effective length of query: 489 Effective length of database: 491 Effective search space: 240099 Effective search space used: 240099 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