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 HSERO_RS11090 HSERO_RS11090 phosphoribosylglycinamide formyltransferase
Query= SwissProt::P33221 (392 letters) >FitnessBrowser__HerbieS:HSERO_RS11090 Length = 403 Score = 435 bits (1118), Expect = e-126 Identities = 242/395 (61%), Positives = 283/395 (71%), Gaps = 8/395 (2%) Query: 2 TLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINM 61 T LGT L +AT+VMLLGSGELGKEV I QRLGVEVIAVDRY +AP VAHR+HVINM Sbjct: 5 TRLGTPLSSSATKVMLLGSGELGKEVIIALQRLGVEVIAVDRYENAPGHQVAHRAHVINM 64 Query: 62 LDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGL-NVVPCARATKLTMNREGIRRL 120 DG AL ++E EKP IVPEIEAIAT+ L++LEE GL V+P ARA LTMNREGIRRL Sbjct: 65 TDGAALAALIEQEKPDLIVPEIEAIATETLVKLEEAGLARVIPTARAAWLTMNREGIRRL 124 Query: 121 AAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKY 180 A E L L TS YRFADS + A+ IGYPC++KPVMSSSGKGQ+ I +++ AW Y Sbjct: 125 AGETLGLATSPYRFADSLEELKAAIDQIGYPCVIKPVMSSSGKGQSKIDGPDEIESAWNY 184 Query: 181 AQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDG-----VHFCAPVGHRQEDGDYRESWQ 235 A GGR AGRVIVEG + FD+EITLLTV +++ FC P+GH Q GDY ESWQ Sbjct: 185 AAAGGRVDAGRVIVEGFIDFDYEITLLTVRSLNENGDTVTSFCDPIGHVQVKGDYVESWQ 244 Query: 236 PQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQ 295 P M ALE+A++IARKV LGG GLFGVELFV GD V FSEVSPRPHDTGMVT++SQ Sbjct: 245 PHPMPGAALEKARDIARKVTENLGGLGLFGVELFVKGDMVWFSEVSPRPHDTGMVTMVSQ 304 Query: 296 DLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVG-ADLQIRLFG 354 SEF LH +A LGLPV + P ASAVI Q ++ + FD V A+ +IRLFG Sbjct: 305 VQSEFELHAKAILGLPVNTALR-TPGASAVIYGQHEARGIAFDGVAEALRIPGAEIRLFG 363 Query: 355 KPEIDGSRRLGVALATAESVVDAIERAKHAAGQVK 389 KPE RR+GVALA+A++V A RAK AA +VK Sbjct: 364 KPESFARRRMGVALASADNVETARIRAKQAAAKVK 398 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: 465 Number of extensions: 23 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: 403 Length adjustment: 31 Effective length of query: 361 Effective length of database: 372 Effective search space: 134292 Effective search space used: 134292 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