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 AZOBR_RS29810 AZOBR_RS29810 phosphoribosylglycinamide formyltransferase
Query= SwissProt::P33221 (392 letters) >FitnessBrowser__azobra:AZOBR_RS29810 Length = 389 Score = 391 bits (1004), Expect = e-113 Identities = 208/383 (54%), Positives = 263/383 (68%), Gaps = 5/383 (1%) Query: 14 RVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVEL 73 +++LLGSGELGKE I +RLG EVIA D YA+APAM VA + V +MLD DALR + Sbjct: 5 KILLLGSGELGKEFVIAAKRLGCEVIACDSYANAPAMQVADAAEVFSMLDPDALRAAIAK 64 Query: 74 EKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYR 133 P +IVPE+EAI T++L + E+ GL VVP ARA +TMNR+ IR +AA EL L TS YR Sbjct: 65 HTPDFIVPEVEAIRTEVLHEFEDAGLTVVPSARAATMTMNRDRIREVAAVELGLRTSKYR 124 Query: 134 FADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVI 193 +A+S G PC++KPVMSSSGKGQ+ +R+AE+L AW YA R +VI Sbjct: 125 YAESLEEVIAGTEHTGLPCVIKPVMSSSGKGQSTVRTAEELEAAWTYAVANMRGDRRKVI 184 Query: 194 VEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARK 253 VE V F++EITLLTV +G+ FC P+GHRQE GDY+ESWQP M L+ A+++A K Sbjct: 185 VEEFVPFEYEITLLTVRTREGILFCEPIGHRQERGDYQESWQPVPMPTALLDDAKDMAAK 244 Query: 254 VVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVG 313 VV LGGYG+FGVE FV DEV+FSE+SPRPHDTGMVTL+SQ+LSEF LH RA LGLP+ Sbjct: 245 VVDNLGGYGIFGVEFFVTKDEVVFSELSPRPHDTGMVTLLSQNLSEFDLHARAILGLPIP 304 Query: 314 GIRQYGPAASAVILPQLTSQNVTFDNVQNA--VGA---DLQIRLFGKPEIDGSRRLGVAL 368 I GPAASAVIL ++ + + +A VG+ D+ +RLFGKP +RR+GVAL Sbjct: 305 AIHVRGPAASAVILADREAERFAIEGLADAMRVGSAEHDVDVRLFGKPTTRKNRRMGVAL 364 Query: 369 ATAESVVDAIERAKHAAGQVKVQ 391 A DA ERA AA + ++ Sbjct: 365 AAGTDTDDARERALKAASAISIR 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: 394 Number of extensions: 14 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 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