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 AZOBR_RS10455 AZOBR_RS10455 glycine dehydrogenase
Query= curated2:Q9A354 (524 letters) >FitnessBrowser__azobra:AZOBR_RS10455 Length = 522 Score = 715 bits (1846), Expect = 0.0 Identities = 364/526 (69%), Positives = 413/526 (78%), Gaps = 8/526 (1%) Query: 1 MNNVGRPTRPEAANDAANGHETLTGARGLLQDEALIFELDGWNKTGVDLPPVTAAPSSDL 60 MNN GRPT +D+A +T+TG RGL +E LIFE D + GVDLP V A +S L Sbjct: 3 MNNQGRPTGLAEGSDSAVP-QTVTGNRGLQIEEPLIFEQDSVGRCGVDLPEVPAV-ASRL 60 Query: 61 NGLLRDAPIGLPGLSEPETVRHYVRLSQKNHAIDLALYPLGSCTMKHNPRLNEKMARLPG 120 + IGLPGL+EP+ VRHY RLSQKN+AID LYPLGSCTMKHNPRLNEKMARLPG Sbjct: 61 GAVKPRGRIGLPGLAEPQVVRHYTRLSQKNYAIDSGLYPLGSCTMKHNPRLNEKMARLPG 120 Query: 121 FSDIHPLQPQSTVQGALELMDRLAHWLKTLTGMPAVALTPKAGAHGELCGLLAIRAAHEA 180 F+D+HPLQP+STVQGALELM L WL TLTGM AV L P AGAHGE+CG++AIR+AH+A Sbjct: 121 FADVHPLQPESTVQGALELMAELGRWLATLTGMAAVTLAPAAGAHGEMCGIMAIRSAHDA 180 Query: 181 AGNGHRKTVLAPTSAHGTNPATAAFVGYTVVEIAQTEDGRVDLADLESKLGDHVAAIMVT 240 G+ R +L P SAHGTNPATAA GY V I TEDGRVDL L++KLG VA +M+T Sbjct: 181 KGDKGRTKILVPESAHGTNPATAAACGYAVEAIPATEDGRVDLEALKAKLGPDVAGLMLT 240 Query: 241 NPNTCGLFERDVVEIARLTHAAGAYFYCDGANFNAIVGRVRPGDLGVDAMHINLHKTFST 300 NPNTCGLFERD++ IA HAAGAYFYCDGANFNAIVGRVRP DLG+D MHINLHKTFST Sbjct: 241 NPNTCGLFERDIITIAEAVHAAGAYFYCDGANFNAIVGRVRPADLGIDVMHINLHKTFST 300 Query: 301 PHGGGGPGAGPVVLSEALAPFAPTPWLTHG-DNGFELAEHAGDDDAKTAFGRMSAFHGQM 359 PHGGGGPG+GPVV +E+LAPF P P++ D F L E AGD AFGRM AFHGQM Sbjct: 301 PHGGGGPGSGPVVFAESLAPFVPVPYVVQDKDGAFRLVEQAGDG---PAFGRMKAFHGQM 357 Query: 360 GMYVRAYAYMLSHGADGLRQVAEDAVLNANYIKAQLKDVMSPAFPEGPCMHEALFDDSWL 419 GM+VRA AYM+SHGADGLRQVA DAVLNANY+ A+L+DVM+P+F EGPCMHE LFDD +L Sbjct: 358 GMFVRALAYMMSHGADGLRQVANDAVLNANYLLARLQDVMTPSF-EGPCMHECLFDDRFL 416 Query: 420 EGTGVTTLDFAKAMIDEGFHPMTMYFPLVVHGAMLIEPTETESKHELDRFIAALRALAGA 479 +GTGVTTLD AKA+IDEGFHPMTMYFPLVVHGA+LIEPTETESK LD+F+ ALRALA Sbjct: 417 KGTGVTTLDIAKALIDEGFHPMTMYFPLVVHGALLIEPTETESKASLDQFVTALRALAER 476 Query: 480 AKAGDTERFKGAPFHAPLRRLDETQAARKPRLRWKP-VAAAPLAAE 524 AK+GD F+GAP P RRLDET AARKP LRW P V +AAE Sbjct: 477 AKSGDVAYFQGAPRLTPRRRLDETAAARKPVLRWSPAVEPEKVAAE 522 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: 916 Number of extensions: 37 Number of successful extensions: 5 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: 522 Length adjustment: 35 Effective length of query: 489 Effective length of database: 487 Effective search space: 238143 Effective search space used: 238143 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