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_045583071.1 AL072_RS16975 formate-dependent phosphoribosylglycinamide formyltransferase
Query= SwissProt::P33221 (392 letters) >NCBI__GCF_001305595.1:WP_045583071.1 Length = 389 Score = 384 bits (986), Expect = e-111 Identities = 202/383 (52%), Positives = 257/383 (67%), Gaps = 5/383 (1%) Query: 14 RVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVEL 73 +++LLGSGELGKE I +RLG EVIA D YA+APAM VA + V +MLD DALR + Sbjct: 5 KILLLGSGELGKEFVIAAKRLGCEVIACDSYANAPAMQVADAAEVFSMLDADALRAAIAK 64 Query: 74 EKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYR 133 P YIVPE+EAI T++L + EE G VVP ARA +TMNR+ IR +AA EL L TS YR Sbjct: 65 HHPDYIVPEVEAIRTEVLHEFEEAGTTVVPSARAATMTMNRDRIREVAAAELGLRTSRYR 124 Query: 134 FADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVI 193 +A+S R G+PC++KPVMSSSGKGQ+ ++ A+ L AW YA R +VI Sbjct: 125 YAESLDEVRAGAEHTGFPCVIKPVMSSSGKGQSTVQDADGLEAAWDYAVANMRGDRRKVI 184 Query: 194 VEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARK 253 VE V F++EITLLTV DG+ +C P+GHRQE GDY+ESWQP M L+ A+ +A + Sbjct: 185 VEEFVPFEYEITLLTVRTRDGILYCEPIGHRQERGDYQESWQPVAMPQRMLDDAKAMAAR 244 Query: 254 VVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVG 313 VV LGGYG+FGVE FV DEV+FSE+SPRPHDTGMVTL+SQ+LSEF LH RA LGLP+ Sbjct: 245 VVDNLGGYGIFGVEFFVTADEVVFSELSPRPHDTGMVTLLSQNLSEFELHARAILGLPIP 304 Query: 314 GIRQYGPAASAVILPQLTSQNVTFDNVQNAVG-----ADLQIRLFGKPEIDGSRRLGVAL 368 I +ASAVIL ++ + + A+ ++ +RLFGKP +RR+GVAL Sbjct: 305 SITCRASSASAVILADREAETFRIEGLSGALSLGSAEQEVDVRLFGKPTTRKNRRMGVAL 364 Query: 369 ATAESVVDAIERAKHAAGQVKVQ 391 A DA RAK AA +V ++ Sbjct: 365 AAGSDTDDARARAKQAADKVTIR 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: 376 Number of extensions: 11 Number of successful extensions: 2 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: 389 Length adjustment: 31 Effective length of query: 361 Effective length of database: 358 Effective search space: 129238 Effective search space used: 129238 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