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_011781828.1 MVAN_RS23500 phosphoribosylglycinamide formyltransferase 2
Query= SwissProt::P33221 (392 letters) >NCBI__GCF_000015305.1:WP_011781828.1 Length = 400 Score = 410 bits (1053), Expect = e-119 Identities = 234/396 (59%), Positives = 271/396 (68%), Gaps = 9/396 (2%) Query: 1 MTLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVIN 60 MT +GT L P AT+VMLLGSGELG+EV I QRLGVE IAVDRY +AP VAH + I Sbjct: 1 MTTIGTPLSPRATKVMLLGSGELGREVLIALQRLGVETIAVDRYDNAPGQQVAHHARTIA 60 Query: 61 MLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLN-VVPCARATKLTMNREGIRR 119 M D D LR ++E E+P +VPEIEAIAT L LE EG+ V+P ARA +LTM+REGIRR Sbjct: 61 MTDPDQLRALIEAERPDLVVPEIEAIATPALEALEAEGVTTVIPTARAARLTMDREGIRR 120 Query: 120 LAAEELQLPTSTYRFADS-ESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAW 178 LAAE L LPTS YRF DS E L IGYPC+VKPVMSSSGKGQ+ I E +A AW Sbjct: 121 LAAETLGLPTSPYRFCDSLEELTAAIEGGIGYPCVVKPVMSSSGKGQSKIDGPEGVAAAW 180 Query: 179 KYAQQGGRAGAGRVIVEGVVKFDFEITLLTVSA--VDG---VHFCAPVGHRQEDGDYRES 233 +YA G R R+IVEG V FD+EITLLTV A DG FC P+GHRQ GDY ES Sbjct: 181 EYAMSGSRVSNTRIIVEGFVDFDYEITLLTVRARGADGEIETRFCEPIGHRQVSGDYVES 240 Query: 234 WQPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLI 293 WQP M ALERA++IA V LGG G+FGVELFV GD+V FSEVSPRPHDTGMVT++ Sbjct: 241 WQPHPMPGTALERARQIAGAVTRDLGGQGIFGVELFVKGDQVWFSEVSPRPHDTGMVTMV 300 Query: 294 SQDLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGA-DLQIRL 352 +Q +EF LH RA LGLPV + P ASAVI + ++ V FD V A+ IRL Sbjct: 301 TQWQNEFELHARAILGLPVDTTLK-SPGASAVIYGGVDAEGVVFDGVDLALRVPHTDIRL 359 Query: 353 FGKPEIDGSRRLGVALATAESVVDAIERAKHAAGQV 388 FGKPE +RR+GVALA A+ V A A AAG+V Sbjct: 360 FGKPESFVNRRMGVALAFADDVDTARRNAAEAAGRV 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: 483 Number of extensions: 32 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 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