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 RR42_RS22745 RR42_RS22745 phosphoribosylglycinamide formyltransferase
Query= SwissProt::P33221 (392 letters) >FitnessBrowser__Cup4G11:RR42_RS22745 Length = 386 Score = 401 bits (1030), Expect = e-116 Identities = 225/382 (58%), Positives = 265/382 (69%), Gaps = 9/382 (2%) Query: 16 MLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVELEK 75 MLLGSGELGKEV I QRLGVE IAVDRYADAP VAH + I+M D D L+ ++E EK Sbjct: 1 MLLGSGELGKEVLIALQRLGVETIAVDRYADAPGQQVAHHARTISMSDPDQLKALIEAEK 60 Query: 76 PHYIVPEIEAIATDMLIQLEEEGL-NVVPCARATKLTMNREGIRRLAAEELQLPTSTYRF 134 P +VPEIEAIAT ML LE G+ V+P ARA +LTM+REGIRRLAAE L +PTS Y+F Sbjct: 61 PDLVVPEIEAIATQMLETLEAAGVVRVIPTARAARLTMDREGIRRLAAETLGVPTSPYKF 120 Query: 135 ADSESLFREAV-ADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVI 193 DS + A+ IGYPC+VKPVMSSSGKGQ+ I + AW YA GGR GRVI Sbjct: 121 CDSLEELQAAIDGGIGYPCVVKPVMSSSGKGQSKIDGPADVKAAWDYAMAGGRVSHGRVI 180 Query: 194 VEGVVKFDFEITLLTVSAV--DG---VHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQ 248 VEG + FD+EITLLTV A+ DG FC P+GH Q GDY ESWQP M P AL+++Q Sbjct: 181 VEGFIDFDYEITLLTVRAIGADGQVETQFCEPIGHVQVSGDYVESWQPHPMHPAALQKSQ 240 Query: 249 EIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFL 308 +IA+ V LGG GLFGVELFV G++V FSEVSPRPHDTGMVT+I+Q +EF LH RA L Sbjct: 241 QIAQAVTANLGGQGLFGVELFVKGEQVWFSEVSPRPHDTGMVTMITQWQNEFELHARAIL 300 Query: 309 GLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGA-DLQIRLFGKPEIDGSRRLGVA 367 GLPV + P ASAVI + ++ V FD V A+ ++RLFGKPE RR+GVA Sbjct: 301 GLPVSTALK-SPGASAVIYGGVDAKGVVFDGVDEALRVPQTELRLFGKPESFTKRRMGVA 359 Query: 368 LATAESVVDAIERAKHAAGQVK 389 LA V A RAK AAG+VK Sbjct: 360 LAYDADVEAARVRAKDAAGRVK 381 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: 442 Number of extensions: 24 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: 392 Length of database: 386 Length adjustment: 30 Effective length of query: 362 Effective length of database: 356 Effective search space: 128872 Effective search space used: 128872 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