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_011802937.1 PNAP_RS17820 phosphoribosylglycinamide formyltransferase 2
Query= SwissProt::P33221 (392 letters) >NCBI__GCF_000015505.1:WP_011802937.1 Length = 401 Score = 402 bits (1033), Expect = e-117 Identities = 231/397 (58%), Positives = 271/397 (68%), Gaps = 9/397 (2%) Query: 1 MTLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVIN 60 MT GT L P AT+VMLLGSGELGKEV I QRLGVE IAVDRY +AP VAH + I Sbjct: 1 MTTFGTPLSPHATKVMLLGSGELGKEVLIALQRLGVETIAVDRYENAPGQQVAHHARTIT 60 Query: 61 MLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEG-LNVVPCARATKLTMNREGIRR 119 M D L+ ++E EKP +VPEIEAIAT ML +LE G + V+P ARA +LTM+REGIRR Sbjct: 61 MSDPAQLKALIEQEKPDLVVPEIEAIATGMLEELEAAGTVRVIPTARAARLTMDREGIRR 120 Query: 120 LAAEELQLPTSTYRFADSESLFREAV-ADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAW 178 LAAE L LPTS Y F DS + A+ + IGYPC+VKPVMSSSGKGQ+ I + +A AW Sbjct: 121 LAAETLALPTSPYVFCDSLEELQTAIDSKIGYPCVVKPVMSSSGKGQSKIALPKDVAPAW 180 Query: 179 KYAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAV--DG---VHFCAPVGHRQEDGDYRES 233 +A GGR GRVIVEG V F++EITLLTV A+ DG HFC P+GH Q GDY ES Sbjct: 181 DHAMAGGRVSRGRVIVEGFVDFEYEITLLTVRALGADGQVETHFCEPIGHLQVSGDYVES 240 Query: 234 WQPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLI 293 WQP M P ALE++ EIAR V L G G+FGVELFV GDEV FSEVSPRPHDTGMVTL Sbjct: 241 WQPHPMRPAALEKSHEIARAVTDNLSGQGVFGVELFVKGDEVWFSEVSPRPHDTGMVTLC 300 Query: 294 SQDLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGA-DLQIRL 352 +Q +EF LH RA LGLPV + P ASAVI + + + FD V +A+ + IRL Sbjct: 301 TQWQNEFELHARAILGLPVDTALK-SPGASAVIYGGVDAAGIVFDGVADALRVPNTDIRL 359 Query: 353 FGKPEIDGSRRLGVALATAESVVDAIERAKHAAGQVK 389 FGKPE RR+GVALA V A A+ AA +V+ Sbjct: 360 FGKPESFVKRRMGVALAFDADVDVARTHARLAASKVR 396 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: 467 Number of extensions: 24 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: 401 Length adjustment: 31 Effective length of query: 361 Effective length of database: 370 Effective search space: 133570 Effective search space used: 133570 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