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 Ac3H11_4666 Phosphoribosylglycinamide formyltransferase 2 (EC 2.1.2.-)
Query= SwissProt::P33221 (392 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4666 Length = 400 Score = 412 bits (1058), Expect = e-119 Identities = 235/398 (59%), Positives = 274/398 (68%), Gaps = 13/398 (3%) Query: 1 MTLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVIN 60 MT LGT L P AT+VMLLGSGELGKEV I QRLGVE IAVDRY +AP VAH + I Sbjct: 1 MTTLGTPLSPHATKVMLLGSGELGKEVLIALQRLGVETIAVDRYDNAPGQQVAHHARTIT 60 Query: 61 MLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEG-LNVVPCARATKLTMNREGIRR 119 M D L+ ++E E+PH +VPEIEAIAT ML +LE G + V+P ARA +LTM+REGIR Sbjct: 61 MSDPAQLKALIEAERPHLVVPEIEAIATPMLEELEAAGTVRVIPTARAARLTMDREGIRV 120 Query: 120 LAAEELQLPTSTYRFADSESLFREAV-ADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAW 178 LAAE L LPTS Y+F +S + A+ A IGYPCIVKPVMSSSGKGQ+ I E + +AW Sbjct: 121 LAAETLGLPTSPYKFCNSLEELQAAIDAGIGYPCIVKPVMSSSGKGQSKIDVPEDVQKAW 180 Query: 179 KYAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDG-----VHFCAPVGHRQEDGDYRES 233 YA GGR GRVIVEG + FD+EIT LTV +V FC P+GH Q GDY ES Sbjct: 181 DYAMAGGRVSHGRVIVEGFIDFDYEITQLTVRSVGAEGQIVTSFCDPIGHVQVSGDYVES 240 Query: 234 WQPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLI 293 WQP M P ALE++++IA+ V LGG GLFGVELFV G+ V FSEVSPRPHDTG+VTL Sbjct: 241 WQPHPMHPAALEKSRQIAKAVTDNLGGQGLFGVELFVKGENVWFSEVSPRPHDTGLVTLC 300 Query: 294 SQDLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAV---GADLQI 350 +Q SEF LH RA LGLPV R P ASAVI + +Q + FD V+ A+ G DL Sbjct: 301 TQHQSEFELHARAILGLPV-DTRLRNPGASAVIYGGVEAQGIVFDGVEEALRVPGTDL-- 357 Query: 351 RLFGKPEIDGSRRLGVALATAESVVDAIERAKHAAGQV 388 RLFGKPE RR+GVALA AE V A AK AAG+V Sbjct: 358 RLFGKPESFVKRRMGVALARAEDVDTARHNAKLAAGKV 395 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: 23 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: 400 Length adjustment: 31 Effective length of query: 361 Effective length of database: 369 Effective search space: 133209 Effective search space used: 133209 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