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_009120825.1 BUB52_RS09320 formate-dependent phosphoribosylglycinamide formyltransferase
Query= SwissProt::P33221 (392 letters) >NCBI__GCF_900129655.1:WP_009120825.1 Length = 388 Score = 348 bits (893), Expect = e-100 Identities = 198/385 (51%), Positives = 256/385 (66%), Gaps = 8/385 (2%) Query: 14 RVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVEL 73 +++LLGSGELGKE I QR G +IA D YA APAM VA V +MLDGDAL RVV Sbjct: 3 KILLLGSGELGKEFVISAQRKGQYIIACDSYAGAPAMQVADECEVFSMLDGDALERVVRK 62 Query: 74 EKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYR 133 +P IVPEIEAI T+ L E+EG+ VVP ARA TMNR+ IR LAA+EL L T+ Y Sbjct: 63 HRPDIIVPEIEAIRTERLYDFEKEGIQVVPSARAVNFTMNRKAIRDLAAKELGLKTAKYF 122 Query: 134 FADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVI 193 +A S + A IG+PC+VKP+MSSSGKGQ+ ++SA++L AW+Y G R +I Sbjct: 123 YATSLDELKAAAEKIGFPCVVKPLMSSSGKGQSLVKSADELEHAWEYGCNGSRGDIKELI 182 Query: 194 VEGVVKFDFEITLLTVSAVDG-VHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIAR 252 +E +KFD EITLLTV+ +G FC P+GH Q+ GDYRES+QP + P L+ AQ++A Sbjct: 183 IEEFIKFDSEITLLTVTQKNGPTLFCPPIGHVQKGGDYRESFQPAHIDPAHLKEAQDMAE 242 Query: 253 KVVLALGGYGLFGVELFVCGDE-VIFSEVSPRPHDTGMVTLI-SQDLSEFALHVRAFLGL 310 KV AL G GL+GVE F+ + V FSE+SPRPHDTGMVTL +Q+L+EF LH RA LGL Sbjct: 243 KVTRALTGAGLWGVEFFLSHENGVYFSELSPRPHDTGMVTLAGTQNLNEFELHCRAVLGL 302 Query: 311 PVGGIRQYGPAASAVILPQLTSQ-NVTFDNVQN-AVGADLQIRLFGKPEIDGSRRLGVAL 368 P+ GI+Q ASAVIL + SQ + ++ A D +R+FGKP +RR+GV L Sbjct: 303 PIPGIKQERIGASAVILSSIASQERPNYRGMEEVAKEEDTYLRIFGKPTTRVNRRMGVVL 362 Query: 369 ATAE--SVVDAI-ERAKHAAGQVKV 390 A S +D + ++AK A +V+V Sbjct: 363 CYAPLGSDLDTLRDKAKRIAEKVEV 387 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: 364 Number of extensions: 14 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: 388 Length adjustment: 31 Effective length of query: 361 Effective length of database: 357 Effective search space: 128877 Effective search space used: 128877 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