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_012276049.1 SHAL_RS04710 formate-dependent phosphoribosylglycinamide formyltransferase
Query= SwissProt::P33221 (392 letters) >NCBI__GCF_000019185.1:WP_012276049.1 Length = 391 Score = 515 bits (1327), Expect = e-151 Identities = 258/389 (66%), Positives = 312/389 (80%), Gaps = 1/389 (0%) Query: 3 LLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINML 62 ++GTAL A R MLLG GELGKEVAIE QR G+EVI VDRY +APAM +AHRSHVINML Sbjct: 1 MIGTALCANAKRAMLLGCGELGKEVAIELQRYGIEVIGVDRYPNAPAMQIAHRSHVINML 60 Query: 63 DGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAA 122 D +AL+ ++ELEKP ++PE+EAIAT L+++E +G+N+VP A+AT+LTM+REGIRRLAA Sbjct: 61 DAEALKALIELEKPDLVIPELEAIATQTLVEMEAKGVNIVPTAKATQLTMDREGIRRLAA 120 Query: 123 EELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQ 182 E L +PTS Y F D+ F AVA IG PC+VKPVMSSSGKGQ+ IR+ EQ+ AW+YAQ Sbjct: 121 ETLAIPTSPYFFCDTLQEFNHAVATIGLPCVVKPVMSSSGKGQSVIRTQEQILAAWQYAQ 180 Query: 183 QGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPL 242 +GGRAG GRVIVEG + FD+EITLLT+SAV+G+HFC +GHRQEDGDYRESWQPQ MS + Sbjct: 181 EGGRAGKGRVIVEGFIAFDYEITLLTISAVNGIHFCDAIGHRQEDGDYRESWQPQVMSDV 240 Query: 243 ALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFAL 302 L ++Q I +KVV ALGGYGLFGVELF+ GDEV FSEVSPRPHDTGMVTLISQDLSEFAL Sbjct: 241 VLAKSQAIGKKVVEALGGYGLFGVELFIKGDEVYFSEVSPRPHDTGMVTLISQDLSEFAL 300 Query: 303 HVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNA-VGADLQIRLFGKPEIDGS 361 HVRA LGLP+ I Q+GP+ASAVIL + S N+ F V A V + Q+RLF KPEIDG Sbjct: 301 HVRAILGLPISNIAQHGPSASAVILAEGKSSNIQFSGVAQALVEPNTQVRLFAKPEIDGR 360 Query: 362 RRLGVALATAESVVDAIERAKHAAGQVKV 390 RRLGV LA ++ A+E+A +AA ++ V Sbjct: 361 RRLGVVLARDINIDKAVEKALNAASKINV 389 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: 459 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: 391 Length adjustment: 31 Effective length of query: 361 Effective length of database: 360 Effective search space: 129960 Effective search space used: 129960 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