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 6937805 Sama_1946 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq)
Query= curated2:A9GBI6 (270 letters) >FitnessBrowser__SB2B:6937805 Length = 245 Score = 111 bits (277), Expect = 2e-29 Identities = 75/230 (32%), Positives = 117/230 (50%), Gaps = 7/230 (3%) Query: 6 IIPCLDVKDGRVVK---GVRFVGLRDAGDPVEAARRYDAEGADEITFLDITASHEKRGII 62 IIP +D+ DG+VV+ G + DP Y +GA + +D+T + + Sbjct: 2 IIPAIDLIDGQVVRLFQGDYAKKTEFSLDPKNQLLSYQQDGAALLHLVDLTGAKDPDKRQ 61 Query: 63 LDVVARTAEVLFTPLTVGGGVKSEQDIKALLDAGADKVAINTAAVNDPDLVRRAADRWGA 122 ++ A L TPL VGGG++S D+ ALL+AG +V I + AV P++V R D++G Sbjct: 62 TKLIEEIAASLSTPLQVGGGIRSAADVDALLNAGVARVVIGSLAVKSPEVVLRLFDKYGG 121 Query: 123 QAIVVAIDARRIADPSRVAWTVVTHGGRRDTGRDAVAWAEEIARAGAGELLVTSMDRDGT 182 AI +A+D AD +++ V HG ++ G+ + + AG LVT + RDGT Sbjct: 122 DAICLALDVNIDADGNKM---VAVHGWQQGGGKSLESLVDTFMPAGLKHALVTDISRDGT 178 Query: 183 RDGYDLLLTAAIA-RAVPVPVIASGGVGTLDHLRAGLVEGGADAALAASI 231 G + L +A R V ASGGV TLD ++A G + + ++ Sbjct: 179 MTGANTALYCELAERFNEVQWQASGGVATLDDVKAVKTSGASGIIIGKAL 228 Score = 23.9 bits (50), Expect = 0.004 Identities = 12/40 (30%), Positives = 19/40 (47%) Query: 81 GGVKSEQDIKALLDAGADKVAINTAAVNDPDLVRRAADRW 120 GGV + D+KA+ +GA + I A + + A W Sbjct: 203 GGVATLDDVKAVKTSGASGIIIGKALLTGVFSAKEAIACW 242 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: 160 Number of extensions: 14 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 270 Length of database: 245 Length adjustment: 24 Effective length of query: 246 Effective length of database: 221 Effective search space: 54366 Effective search space used: 54366 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