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_024891040.1 Z164_RS0112570 formate-dependent phosphoribosylglycinamide formyltransferase
Query= SwissProt::P33221 (392 letters) >NCBI__GCF_000559025.1:WP_024891040.1 Length = 404 Score = 472 bits (1214), Expect = e-138 Identities = 258/398 (64%), Positives = 294/398 (73%), Gaps = 15/398 (3%) Query: 1 MTLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVIN 60 M LGT L P+ATRV+LLGSGELGKEVAIE QR G EVIA DRYADAPAM VAHRSHV++ Sbjct: 1 MVRLGTPLSPSATRVLLLGSGELGKEVAIELQRFGAEVIAADRYADAPAMQVAHRSHVLD 60 Query: 61 MLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEE------GLNVVPCARATKLTMNR 114 MLDG A+R +V E+PH IVPEIEAI T L+ LE E V+P ARA +LTM+R Sbjct: 61 MLDGAAIRALVAHERPHLIVPEIEAIHTPTLVALEREFAEAGTATRVIPTARAARLTMDR 120 Query: 115 EGIRRLAAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQL 174 EGIRRLAAE L LPTS YRF DS +R AVA+IG PC+VKPVMSSSGKGQ+ +R A Q+ Sbjct: 121 EGIRRLAAETLGLPTSPYRFVDSLEDYRAAVAEIGLPCVVKPVMSSSGKGQSLVREAAQV 180 Query: 175 AQAWKYAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESW 234 AW +AQ GGRAGAGRVIVEG V FD+EITLLTV G FCAP+GH Q DGDYRESW Sbjct: 181 DGAWDHAQTGGRAGAGRVIVEGFVDFDYEITLLTVRHAGGTAFCAPIGHLQRDGDYRESW 240 Query: 235 QPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLIS 294 QPQ MSPLAL R+QEIAR + LGG+G+FGVELFV GDEV FSEVSPRPHDTG+VTL S Sbjct: 241 QPQPMSPLALARSQEIARAITDDLGGWGVFGVELFVKGDEVWFSEVSPRPHDTGLVTLAS 300 Query: 295 QDLSEFALHVRAFLGLPV-----GGIRQYGPAASAVILPQLTSQNV-TFDNVQNAVGA-D 347 Q+LSEFALH RA LGLPV G + GPAAS +L Q V F NV+ A+ A Sbjct: 301 QELSEFALHARAILGLPVPADADGTVPLLGPAASCALLAQ--GHGVPAFANVEAALRAPG 358 Query: 348 LQIRLFGKPEIDGSRRLGVALATAESVVDAIERAKHAA 385 +RLFGKP ++G RR+GV LA A+ V A A+ AA Sbjct: 359 TALRLFGKPRVEGQRRVGVTLARAQDVEAARATAREAA 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: 514 Number of extensions: 22 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: 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 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