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 BPHYT_RS06125 BPHYT_RS06125 phosphoribosylglycinamide formyltransferase
Query= SwissProt::P33221 (392 letters) >FitnessBrowser__BFirm:BPHYT_RS06125 Length = 404 Score = 450 bits (1158), Expect = e-131 Identities = 245/394 (62%), Positives = 285/394 (72%), Gaps = 9/394 (2%) Query: 4 LGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLD 63 +GT L +ATRVMLLG+GELGKEV I QRLGVEVIAVDRY +AP VAHR+HVI+M D Sbjct: 7 IGTPLSESATRVMLLGAGELGKEVIIALQRLGVEVIAVDRYPNAPGHQVAHRAHVIDMTD 66 Query: 64 GDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGL-NVVPCARATKLTMNREGIRRLAA 122 ALR +VE E+PH IVPEIEAIATD L +E +GL V+P ARAT+LTMNREGIRRLAA Sbjct: 67 RAALRALVEQERPHLIVPEIEAIATDALAAIESDGLAEVIPTARATQLTMNREGIRRLAA 126 Query: 123 EELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQ 182 EEL LPTS Y FADS R +A +GYPC+VKPVMSSSGKGQ+ +RS + AW+YA Sbjct: 127 EELGLPTSPYAFADSLDELRAGIAKVGYPCVVKPVMSSSGKGQSVLRSDADVEPAWQYAL 186 Query: 183 QGGRAGAGRVIVEGVVKFDFEITLLTVSAVD------GVHFCAPVGHRQEDGDYRESWQP 236 GGR GRVIVEG + F++EIT LTV A+D +FC P+GH Q GDY ESWQP Sbjct: 187 AGGRVNHGRVIVEGFIDFEYEITQLTVRAIDPASGEVSTYFCDPIGHVQVAGDYVESWQP 246 Query: 237 QQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQD 296 Q MSPLALER++E+A KV ALGG GLFGVELFV GD+V FSEVSPRPHDTG+VTL SQ Sbjct: 247 QPMSPLALERSREVAHKVTAALGGRGLFGVELFVRGDDVWFSEVSPRPHDTGLVTLCSQR 306 Query: 297 LSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGA-DLQIRLFGK 355 SEF LH RA LGLPV + P ASAVI L + F+ V A+ + +RLFGK Sbjct: 307 FSEFELHARAILGLPVDTSLR-APGASAVIYGGLDEAGIAFEGVAAALAVPNADLRLFGK 365 Query: 356 PEIDGSRRLGVALATAESVVDAIERAKHAAGQVK 389 PE RR+GVALAT E+ +A RAK AA V+ Sbjct: 366 PESFAKRRMGVALATGENTDEARSRAKQAAAAVR 399 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: 454 Number of extensions: 15 Number of successful extensions: 5 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: 404 Length adjustment: 31 Effective length of query: 361 Effective length of database: 373 Effective search space: 134653 Effective search space used: 134653 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