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 BWI76_RS18945 BWI76_RS18945 1-(5-phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole-4- carboxamide isomerase
Query= curated2:B2A6X0 (251 letters) >FitnessBrowser__Koxy:BWI76_RS18945 Length = 245 Score = 115 bits (288), Expect = 8e-31 Identities = 70/209 (33%), Positives = 113/209 (54%), Gaps = 5/209 (2%) Query: 6 IIPCLDVKDGQVVK---GVKFNELKLAGDPVELAQKYDREGADELVFLDITASIEDRGTM 62 IIP LD+ DG VV+ G + DP+ Q Y +GA+ L +D+T + + Sbjct: 2 IIPALDLIDGTVVRLHQGDYGQQRDYGNDPLPRLQSYAAQGAEVLHLVDLTGAKDPAKRQ 61 Query: 63 LEVVEKTAKNVFIPFTVGGGIKTVDDMRRLLQAGADKVSINSAAVKNPELISQGSDRFGS 122 + +++K V +P VGGG++T D+ LL+AG +V + S AVK+PE++ RFG Sbjct: 62 IPLLKKLVAGVNVPVQVGGGVRTEQDVAALLEAGVARVVVGSTAVKSPEVVKGWFKRFGP 121 Query: 123 QCIVVAIDTKKTEEG-YQVFINGGTKNTGIPLMDWVKEVKYRGAGEILLTSIDHDGGKNG 181 Q +V+A+D + EG QV ++G +N+G+ L + V+ + G +L T I DG G Sbjct: 122 QHLVLALDVRIDAEGRKQVAVSGWQENSGVTLEELVESYQSVGLQHVLCTDISRDGTLAG 181 Query: 182 YDNDIINQV-ARVSNIPVIASGGAGTIED 209 + + +V AR + +SGG G + D Sbjct: 182 SNVSLYEEVCARYPQVAFQSSGGIGDLND 210 Score = 24.3 bits (51), Expect = 0.003 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 2/74 (2%) Query: 162 YRGAGEILLTSIDHDGGKNGYDNDI--INQVARVSNIPVIASGGAGTIEDFYNVFHKGQA 219 Y G +L +D G K+ I + ++ N+PV GG T +D + G A Sbjct: 38 YAAQGAEVLHLVDLTGAKDPAKRQIPLLKKLVAGVNVPVQVGGGVRTEQDVAALLEAGVA 97 Query: 220 SGALAASVFHFEEI 233 + ++ E+ Sbjct: 98 RVVVGSTAVKSPEV 111 Lambda K H 0.316 0.137 0.383 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: 145 Number of extensions: 9 Number of successful extensions: 3 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: 251 Length of database: 245 Length adjustment: 24 Effective length of query: 227 Effective length of database: 221 Effective search space: 50167 Effective search space used: 50167 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 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