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 WP_011777960.1 MVAN_RS03460 formate-dependent phosphoribosylglycinamide formyltransferase
Query= SwissProt::P33221 (392 letters) >NCBI__GCF_000015305.1:WP_011777960.1 Length = 379 Score = 252 bits (643), Expect = 1e-71 Identities = 155/388 (39%), Positives = 222/388 (57%), Gaps = 33/388 (8%) Query: 15 VMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVELE 74 V+LLG+GE E+A+ + LG +V+ V + + AL +++ Sbjct: 9 VLLLGAGERSSELALAFRHLGADVVTVSDHGET-----------------QALTALIDER 51 Query: 75 KPHYIVPEIEAIATDMLIQL-EEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYR 133 +P Y+V + +ATD LI + E + + V P RAT+L+++ EG+RRLAA+EL LPT+ + Sbjct: 52 RPRYVVADAATVATDALIAVAERDDVEVFPTPRATRLSLDGEGLRRLAADELGLPTAPFW 111 Query: 134 FADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVI 193 FA S VA G+P +VKPV ++ G+G++ + + + AW++A G RVI Sbjct: 112 FAGSVEELTAIVAHAGFPMVVKPVAAAPGEGESVLLRPDDVEPAWRHATAAGNLK--RVI 169 Query: 194 VEGVVKFDFEITLLTV----SAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQE 249 E VV+ DFE+TLLTV +A VHFC P+GH Q D D ESWQPQQ+SP AL+ A+ Sbjct: 170 AETVVEVDFEVTLLTVRTTGAAGPTVHFCEPIGHHQNDDDALESWQPQQLSPTALDSAKS 229 Query: 250 IARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLG 309 IA ++V +LGG G+F VEL V GDEV FS+V PR D+G+VTL SQ LS+F LH RA LG Sbjct: 230 IAARIVNSLGGRGVFAVELLVRGDEVYFSDVRPRLQDSGLVTLRSQRLSQFELHARAVLG 289 Query: 310 LPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVG-----ADLQIRLF---GKPEIDGS 361 LPV I P A V P + V ++ + A+ +RLF + D Sbjct: 290 LPVDTI-MISPGAVEVSYPDGEGRAVPDREIRAVLADALAVAESDVRLFPATAAGDDDDV 348 Query: 362 RRLGVALATAESVVDAIERAKHAAGQVK 389 L + ATA+ + A +RA+ A V+ Sbjct: 349 PWLSWSTATAQDPIVARDRARRVATAVR 376 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: 342 Number of extensions: 22 Number of successful extensions: 5 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: 379 Length adjustment: 30 Effective length of query: 362 Effective length of database: 349 Effective search space: 126338 Effective search space used: 126338 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 24 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