Align Imidazole glycerol phosphate synthase subunit HisF; EC 4.3.2.10; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF (uncharacterized)
to candidate N515DRAFT_2933 N515DRAFT_2933 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= curated2:A9GBI6 (270 letters) >FitnessBrowser__Dyella79:N515DRAFT_2933 Length = 242 Score = 100 bits (250), Expect = 2e-26 Identities = 79/247 (31%), Positives = 118/247 (47%), Gaps = 18/247 (7%) Query: 6 IIPCLDVKDGRVVKGVRFVGLRDAG-------DPVEAARRYDAEGADEITFLDITASHEK 58 +IP +D++ GRVV+ + D G +P E ARRY GA + +D+ + Sbjct: 5 VIPAIDLRTGRVVR----LRQGDYGQQTTYEFEPRELARRYAEAGAAWLHVVDLDGARSG 60 Query: 59 RGIILDVVARTAEVLFTPLTVGGGVKSEQDIKALLDAGADKVAINTAAVNDPDLVRRAAD 118 L V+ A + GGGV+SE D++ L DAG +V + + A+ +P LV Sbjct: 61 SLDNLQVIEALARDGMQ-VQAGGGVRSEADLQRLFDAGVARVVVGSVAIREPALVGAWLG 119 Query: 119 RWGAQAIVVAIDARRIADPSRVAWTVVTHGGRRDTGRDAVAWAEEIARAGAGELLVTSMD 178 ++G + VA+D RRI W + + G R A A GA LL T +D Sbjct: 120 KFGTDKLTVALDTRRIDG----RWALPSAGWTELEARSLDELAPWYAARGARHLLCTDID 175 Query: 179 RDGTRDGYDLLLTAAIARAVP-VPVIASGGVGTLDHLRAGLVEGGADAALAASIFHDAEY 237 RDG G++L L +AR P + V ASGGV ++D + A G L ++ + + Sbjct: 176 RDGMLAGFNLELYRDLARTAPTLAVQASGGVRSVDDIVAARAAGAQGVILGRALL-EGRF 234 Query: 238 TIGEAKA 244 TI EA A Sbjct: 235 TIEEALA 241 Lambda K H 0.319 0.136 0.393 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: 176 Number of extensions: 10 Number of successful extensions: 4 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: 270 Length of database: 242 Length adjustment: 24 Effective length of query: 246 Effective length of database: 218 Effective search space: 53628 Effective search space used: 53628 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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