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 WP_092481817.1 BM299_RS02175 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= curated2:B1YL09 (249 letters) >NCBI__GCF_900115975.1:WP_092481817.1 Length = 248 Score = 119 bits (298), Expect = 6e-32 Identities = 73/212 (34%), Positives = 117/212 (55%), Gaps = 13/212 (6%) Query: 6 IIPCLDVKEGRVVKGVKFQNLRDL---GDPVAVAKYYYEQGADELVLLDISATQEGRDTM 62 I P +D++EG+ V+ V+ + R+ DPVAVA+ + GA L ++D+ G Sbjct: 3 IFPAIDLREGKCVRLVEGKLDRETVYSDDPVAVARLWEASGAQWLHVVDLDGAFAGSPKN 62 Query: 63 LDIVERVAEVIYMPFTVGGGIKTLEDAKRLIRAGADKVSLNSSALQNPQLIQDISRLFGV 122 LD ++ + I + VGGGI+ L +RL++ G +V L + A+QNP L+ FG Sbjct: 63 LDTIQEIISAINISVQVGGGIRDLATIERLLQMGVARVILGTVAIQNPALVAQACARFGS 122 Query: 123 QATVVAIDAKR---TGDSWGVFSHGGTQAVGRDAIEWAKEAVSLGAGELLVTSMDADGTK 179 + VV IDA++ + WG + +DA+E A E +GA ++ T + DGT Sbjct: 123 ERIVVGIDARKGKVAIEGWGFTAE-------KDALELADEISRMGATRVVFTDISRDGTL 175 Query: 180 DGYDLELIQRLREVVNVPLIASGGVGTLEHLA 211 G +LE I++L +V + +IASGGV T+E +A Sbjct: 176 KGPNLEAIKKLAQVSKLKVIASGGVSTIEDIA 207 Score = 36.6 bits (83), Expect = 5e-07 Identities = 24/90 (26%), Positives = 46/90 (51%), Gaps = 4/90 (4%) Query: 4 KRIIPCLDVKEGRV-VKGVKFQNLRDLGDPVAVAKYYYEQGADELVLLDISATQEGRDTM 62 +RI+ +D ++G+V ++G F +D + +A GA +V DIS + Sbjct: 123 ERIVVGIDARKGKVAIEGWGFTAEKDA---LELADEISRMGATRVVFTDISRDGTLKGPN 179 Query: 63 LDIVERVAEVIYMPFTVGGGIKTLEDAKRL 92 L+ ++++A+V + GG+ T+ED L Sbjct: 180 LEAIKKLAQVSKLKVIASGGVSTIEDIAAL 209 Score = 25.4 bits (54), Expect = 0.001 Identities = 16/75 (21%), Positives = 32/75 (42%) Query: 152 DAIEWAKEAVSLGAGELLVTSMDADGTKDGYDLELIQRLREVVNVPLIASGGVGTLEHLA 211 D + A+ + GA L V +D +L+ IQ + +N+ + GG+ L + Sbjct: 31 DPVAVARLWEASGAQWLHVVDLDGAFAGSPKNLDTIQEIISAINISVQVGGGIRDLATIE 90 Query: 212 EGLEAGADAALAASI 226 L+ G + ++ Sbjct: 91 RLLQMGVARVILGTV 105 Lambda K H 0.317 0.136 0.380 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: 161 Number of extensions: 10 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 249 Length of database: 248 Length adjustment: 24 Effective length of query: 225 Effective length of database: 224 Effective search space: 50400 Effective search space used: 50400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 10 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