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 BWI76_RS18090 BWI76_RS18090 phosphoribosylglycinamide formyltransferase 2
Query= SwissProt::P33221 (392 letters) >FitnessBrowser__Koxy:BWI76_RS18090 Length = 392 Score = 655 bits (1691), Expect = 0.0 Identities = 334/392 (85%), Positives = 357/392 (91%) Query: 1 MTLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVIN 60 MT+LGTALRPAAT+VMLLGSGELGKEVAIECQRLG+E IAVDRY DAPAM VAHRSHVIN Sbjct: 1 MTVLGTALRPAATKVMLLGSGELGKEVAIECQRLGIETIAVDRYPDAPAMQVAHRSHVIN 60 Query: 61 MLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRL 120 ML G+AL+ ++E EKP +IVPEIEAIATD L+ LE+ G VVP ARA KLTMNREGIRRL Sbjct: 61 MLHGEALQALIEQEKPDFIVPEIEAIATDTLVALEQTGQKVVPTARAAKLTMNREGIRRL 120 Query: 121 AAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKY 180 AAEEL+LPTS YRFADSE FREAVA+IG PCIVKPVMSSSGKGQ+FIRS+EQLA AW+Y Sbjct: 121 AAEELKLPTSAYRFADSEPAFREAVAEIGLPCIVKPVMSSSGKGQSFIRSSEQLADAWQY 180 Query: 181 AQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMS 240 AQQGGRAGAGRVIVEGVV FDFEITLLTVSA DGVHFCAPVGHRQEDGDYRESWQPQQMS Sbjct: 181 AQQGGRAGAGRVIVEGVVNFDFEITLLTVSAADGVHFCAPVGHRQEDGDYRESWQPQQMS 240 Query: 241 PLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEF 300 LALERAQEIAR+VVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEF Sbjct: 241 ALALERAQEIARQVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEF 300 Query: 301 ALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGADLQIRLFGKPEIDG 360 ALHVRAFLGLP+G IRQYGPAASAVILPQLTSQNVTF N+Q AVGA LQ+RLFGKPEIDG Sbjct: 301 ALHVRAFLGLPIGAIRQYGPAASAVILPQLTSQNVTFSNIQAAVGAGLQLRLFGKPEIDG 360 Query: 361 SRRLGVALATAESVVDAIERAKHAAGQVKVQG 392 SRRLGV LA A++V +A+ RAK AA V V G Sbjct: 361 SRRLGVTLAIADNVEEAVTRAKAAASAVIVAG 392 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: 522 Number of extensions: 11 Number of successful extensions: 1 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: 392 Length adjustment: 31 Effective length of query: 361 Effective length of database: 361 Effective search space: 130321 Effective search space used: 130321 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