Align Formate-dependent phosphoribosylglycinamide formyltransferase; 5'-phosphoribosylglycinamide transformylase 2; Formate-dependent GAR transformylase; GAR transformylase 2; GART 2; Non-folate glycinamide ribonucleotide transformylase; Phosphoribosylglycinamide formyltransferase 2; EC 2.1.2.- (characterized)
to candidate 3607265 Dshi_0680 phosphoribosylaminoimidazole carboxylase, ATPase subunit (RefSeq)
Query= SwissProt::P33221 (392 letters) >FitnessBrowser__Dino:3607265 Length = 357 Score = 113 bits (282), Expect = 1e-29 Identities = 109/363 (30%), Positives = 167/363 (46%), Gaps = 20/363 (5%) Query: 8 LRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDAL 67 L P A + +LG G+LG+ +++ RLG + A PA VA D DAL Sbjct: 5 LAPGAV-IGMLGGGQLGRMLSMAAARLGFRCHIFEPGAAPPAGQVAEAVTTAGYDDLDAL 63 Query: 68 RRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQL 127 RR E+ I E E I T L LE + P RA ++ +R + L L Sbjct: 64 RRFAEVVD--VITYEFENIPTAALDVLEALR-PIHPGRRALAVSQDRLTEKEFL-RGLGL 119 Query: 128 PTSTYRFADSESLFREAVADIGYPCIVKPV-MSSSGKGQTFIRSAEQLAQAWKYAQQGGR 186 T+ + D + A+A IG P I+K + GKGQT + + A+A Sbjct: 120 QTAPFAPVDDAAGLEAALAAIGTPAILKTRRLGYDGKGQTRLTAPGDAAEAL-----AAM 174 Query: 187 AGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHR-QEDGDYRESWQPQQMSPLALE 245 AGA I+EG V+F E++++ DG C G DG + P ++S Sbjct: 175 AGAP-AILEGFVEFSHEVSVIAARGQDGAVACFDPGENVHRDGILATTTVPARLSHAQRT 233 Query: 246 RAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVR 305 A +A +++ AL G+ GVELFV +I +E++PR H++G T + +F H+R Sbjct: 234 DAVLLAGRILNALDYVGVMGVELFVTRGGLIVNEIAPRVHNSGHWTQTGCVIDQFEQHIR 293 Query: 306 AFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNV-QNAVGADLQIRLFGKPEIDGSRRL 364 A G P+G G + V++ L ++ D V + A D+ + L+GK E R++ Sbjct: 294 AVAGWPLGD----GQRHADVVMENLIGSDM--DRVPELAAARDVALHLYGKAETRAGRKM 347 Query: 365 GVA 367 G A Sbjct: 348 GHA 350 Lambda K H 0.320 0.136 0.390 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: 292 Number of extensions: 18 Number of successful extensions: 4 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: 392 Length of database: 357 Length adjustment: 30 Effective length of query: 362 Effective length of database: 327 Effective search space: 118374 Effective search space used: 118374 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 (21.8 bits) S2: 50 (23.9 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