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_012284028.1 HM1_RS13860 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= curated2:Q1D4M4 (253 letters) >NCBI__GCF_000019165.1:WP_012284028.1 Length = 245 Score = 107 bits (267), Expect = 2e-28 Identities = 74/240 (30%), Positives = 124/240 (51%), Gaps = 10/240 (4%) Query: 10 LDVKGGRVVK---GVQFEGLRDVGDPVELARRYEAEGADELTFLDISASAEERDTLWELV 66 +D+KGGR V+ G + + DPV A ++A+GA + +D+ + E ++ Sbjct: 7 IDLKGGRCVRLYQGRMEDAIVYNDDPVSQALAWQAKGAQMIHLVDLDGAFEGEPKNLPVI 66 Query: 67 RRTAEQLFIPLAVGGGVRTVDDVGRALRAGADKVSINSAAVANPALLTACAERFGAQCVV 126 + E + + + +GGG+R ++ + R LR G +V I +AA+ NP LL+ + +G Q +V Sbjct: 67 QAILEAVTVAVQLGGGIRDLNIIDRYLRMGVSRVIIGTAAIKNPELLSVACKEYG-QRIV 125 Query: 127 ASIDAKRDGDRWRVYTHGGRKPTDLDAVAWARECVARGAGEVLLTSIDRDGARTGYDLAL 186 +DA RDG +V T G + + A+ A E RG V+ T I +DG G +LA Sbjct: 126 LGLDA-RDG---KVATDGWAGTSQVTALELALEMKGRGLRRVVYTDISKDGTLAGPNLAA 181 Query: 187 TRAVSEAVDVPVIASGGAGSAAHVR--AAFQEGGADAALVAGILHDGVTTVGAIKALLRE 244 T ++ A + VIASGG + V+ AA + G + A++ ++ G V + RE Sbjct: 182 TAELARATGLKVIASGGFATIDDVKAAAALEGDGIEGAILGKSIYTGAIDVAEAIRVARE 241 Lambda K H 0.320 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: 180 Number of extensions: 16 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: 253 Length of database: 245 Length adjustment: 24 Effective length of query: 229 Effective length of database: 221 Effective search space: 50609 Effective search space used: 50609 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: 46 (22.3 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