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_057508859.1 ABB28_RS12030 formate-dependent phosphoribosylglycinamide formyltransferase
Query= SwissProt::P33221 (392 letters) >NCBI__GCF_001431535.1:WP_057508859.1 Length = 395 Score = 481 bits (1239), Expect = e-140 Identities = 254/391 (64%), Positives = 294/391 (75%), Gaps = 1/391 (0%) Query: 1 MTLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVIN 60 M+ GT L P+ATRV+LLGSGELGKEVAIE QRLGVEVIA DRYADAPAM VAHR+HVI+ Sbjct: 1 MSAFGTPLSPSATRVLLLGSGELGKEVAIELQRLGVEVIAADRYADAPAMQVAHRAHVID 60 Query: 61 MLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEE-GLNVVPCARATKLTMNREGIRR 119 MLD ALR ++ LEKPH +VPEIEAI T+ L+QLE+E GL VVP ARA +LTM+REGIRR Sbjct: 61 MLDAMALRELIALEKPHLVVPEIEAIHTETLVQLEQEQGLRVVPTARAARLTMDREGIRR 120 Query: 120 LAAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWK 179 LAAE L LPTS YRF D+E+ + AV IG PC+VKPVMSSSGKGQ+ +RS +A AW Sbjct: 121 LAAETLGLPTSPYRFVDTEAEYIAAVQAIGLPCVVKPVMSSSGKGQSTLRSEADIAPAWA 180 Query: 180 YAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQM 239 YAQ GGRAGAGR IVEG + FD+EITLLTV G FCAP+GH Q+DGDYRESWQPQ M Sbjct: 181 YAQTGGRAGAGRCIVEGFIDFDYEITLLTVRHAGGTSFCAPIGHLQKDGDYRESWQPQAM 240 Query: 240 SPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSE 299 S AL RA+EI+R + LGG+GLFGVELFV GDEV FSEVSPRPHDTG+VTL+SQ+LSE Sbjct: 241 SAAALARAEEISRAITDDLGGWGLFGVELFVKGDEVWFSEVSPRPHDTGLVTLVSQELSE 300 Query: 300 FALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGADLQIRLFGKPEID 359 FALH RA LGLP+ IRQ GP+AS +L D D +RLFGKP + Sbjct: 301 FALHARAILGLPIPVIRQGGPSASCALLAHGEGVPYFTDVAAALQVPDTAVRLFGKPSVH 360 Query: 360 GSRRLGVALATAESVVDAIERAKHAAGQVKV 390 G RR+GV LA A+S A A+ AA + V Sbjct: 361 GHRRVGVTLARADSTDAARAIAREAAAAIGV 391 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: 466 Number of extensions: 23 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: 395 Length adjustment: 31 Effective length of query: 361 Effective length of database: 364 Effective search space: 131404 Effective search space used: 131404 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