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_011371669.1 SUDEN_RS00160 phosphoribosylglycinamide formyltransferase 2
Query= SwissProt::P33221 (392 letters) >NCBI__GCF_000012965.1:WP_011371669.1 Length = 387 Score = 374 bits (961), Expect = e-108 Identities = 198/387 (51%), Positives = 259/387 (66%), Gaps = 3/387 (0%) Query: 3 LLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINML 62 L L+ + ++MLLGSGELG+EVAIE QRLG+EVIAVDRY +APA VAHRS+V+NM Sbjct: 2 LFSAPLKSNSKKIMLLGSGELGREVAIEAQRLGLEVIAVDRYQNAPAHSVAHRSYVVNMQ 61 Query: 63 DGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAA 122 D DAL ++ EKP YI+PEIEAI+ D L + E++G NV+P A A TMNR+ IR AA Sbjct: 62 DKDALLEIIYREKPDYILPEIEAISIDALFEAEDKGYNVIPNANAVSKTMNRKNIRTFAA 121 Query: 123 EELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQ 182 E L+L T Y F ++ + A +G+PC++KPVMSSSG GQ+ RSA + +W+ A+ Sbjct: 122 EVLELKTGAYEFVTTKEMLVSAAGRLGFPCVIKPVMSSSGHGQSVARSASDIDASWEIAK 181 Query: 183 QGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPL 242 + R A +IVE V FD+EIT+LT FC P+GH Q DGDY SWQP QMS + Sbjct: 182 E-ARGDASELIVEAFVDFDYEITMLTARNGKETVFCEPIGHEQRDGDYVFSWQPMQMSEI 240 Query: 243 ALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFAL 302 A +RA+++A+K+ LGG GLFGVELF+ GDEV FSEVSPRPHDTGMVTLI+Q SEFAL Sbjct: 241 AKQRAEDMAKKITDGLGGRGLFGVELFIKGDEVYFSEVSPRPHDTGMVTLITQSQSEFAL 300 Query: 303 HVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGADLQIRLFGKPEIDGSR 362 H+RA LGLP+ YG ASA ++ + + ++ + +R+FGKPE R Sbjct: 301 HLRAVLGLPL-EFTFYGEGASAAFKSEVHNFSPVIHVDESLFSKNSFVRIFGKPEAHKGR 359 Query: 363 RLGVALATAESVVDAIERAKHAAGQVK 389 RL VAL + A++RA+ +VK Sbjct: 360 RLAVAL-VFDKAEQALQRARELITKVK 385 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: 360 Number of extensions: 10 Number of successful extensions: 3 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: 387 Length adjustment: 30 Effective length of query: 362 Effective length of database: 357 Effective search space: 129234 Effective search space used: 129234 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