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 Ga0059261_3259 Ga0059261_3259 Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain
Query= curated2:Q9A354 (524 letters) >FitnessBrowser__Korea:Ga0059261_3259 Length = 522 Score = 658 bits (1698), Expect = 0.0 Identities = 339/517 (65%), Positives = 395/517 (76%), Gaps = 7/517 (1%) Query: 9 RPEAANDAANGHETLTGARGLLQDEALIFELDGWNKTGVDLPPVTAAPSSDLNGLLRDAP 68 RPE A + T TG R L+ DEALIFE+ + TGVD A +S + GL R+ Sbjct: 9 RPEMNAGARSDDATFTGNRALMLDEALIFEIGSLDTTGVDFAEAPKA-ASRIGGLARNKD 67 Query: 69 IGLPGLSEPETVRHYVRLSQKNHAIDLALYPLGSCTMKHNPRLNEKMARLPGFSDIHPLQ 128 IGLPGLSEPE VRHY RLS++N+AIDL L+PLGSCTMKHNPRLNE+MARLPGF+D+HPLQ Sbjct: 68 IGLPGLSEPEAVRHYTRLSRQNYAIDLGLFPLGSCTMKHNPRLNERMARLPGFADVHPLQ 127 Query: 129 PQSTVQGALELMDRLAHWLKTLTGMPAVALTPKAGAHGELCGLLAIRAAHEAAGNGHRKT 188 P TVQGA E++ +LAHWL TLTGM +VA++PKAGAHGELCG+LAIRAA +A G RK Sbjct: 128 PVDTVQGAFEVIHQLAHWLVTLTGMHSVAMSPKAGAHGELCGVLAIRAALDAKGEQARKV 187 Query: 189 VLAPTSAHGTNPATAAFVGYTVVEIAQTEDGRVDLADLESKLGDHVAAIMVTNPNTCGLF 248 +L P SAHGTNPATAAF G+TV +I TE GRVDL L+++LG VA +M+TNPNTCGLF Sbjct: 188 LLVPESAHGTNPATAAFAGFTVEDIPATEAGRVDLEALKARLGPDVAGVMITNPNTCGLF 247 Query: 249 ERDVVEIARLTHAAGAYFYCDGANFNAIVGRVRPGDLGVDAMHINLHKTFSTPHGGGGPG 308 E D+ I+ H AG Y YCDGANFNAIVGRVRPGDLG+DAMHINLHKTFSTPHGGGGPG Sbjct: 248 EPDMKAISDAVHEAGGYVYCDGANFNAIVGRVRPGDLGIDAMHINLHKTFSTPHGGGGPG 307 Query: 309 AGPVVLSEALAPFAPTPWLTHGDNGFELAEH--AGDDDAKTAFGRMSAFHGQMGMYVRAY 366 +GPVVLS ALAP+AP P++ + F L E AG A+ +FGRM +FHGQMGM+ RA Sbjct: 308 SGPVVLSAALAPYAPLPFVEKQGDRFVLIEEETAGTHHAE-SFGRMVSFHGQMGMFTRAL 366 Query: 367 AYMLSHGADGLRQVAEDAVLNANYIKAQLKDVMSPAFPE-GPCMHEALFDDSWLEGTGVT 425 Y+LSHGADGLRQVAED+VLNANY+ L+DV+ F + GPCMHEA+F D L G + Sbjct: 367 TYILSHGADGLRQVAEDSVLNANYVLRALEDVLDAPFAKSGPCMHEAIFSDKGLP-EGFS 425 Query: 426 TLDFAKAMIDEGFHPMTMYFPLVVHGAMLIEPTETESKHELDRFIAALRALAGAAKAGDT 485 TLD AK +IDEGFHPMT+YFPLVVHGAML+EPTETESK LD+FI A R++A AKAGD Sbjct: 426 TLDIAKGLIDEGFHPMTVYFPLVVHGAMLVEPTETESKAALDQFIGAFRSVAERAKAGDA 485 Query: 486 ERFKGAPFHAPLRRLDETQAARKPRLRWKPVAAAPLA 522 K AP AP RRLDETQAARKP L WK A A A Sbjct: 486 -ALKSAPHFAPRRRLDETQAARKPVLVWKEPAQAEAA 521 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: 867 Number of extensions: 27 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: 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