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 NP_347576.1 CA_C0940 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= curated2:Q4FNT7 (251 letters) >NCBI__GCF_000008765.1:NP_347576.1 Length = 239 Score = 116 bits (291), Expect = 4e-31 Identities = 76/230 (33%), Positives = 125/230 (54%), Gaps = 16/230 (6%) Query: 6 IIPCLDVKNGRVVKGINFVDLKD---AGDPVEQAKIYSDGGADEICFLDITASKE----N 58 I+P +D+K G+ V+ K A P AK + + GA I +D+ + E N Sbjct: 3 ILPAIDIKQGKCVRLYQGRFEKSSVVAESPALTAKSFENDGAKYIHVVDLDGALEGEIIN 62 Query: 59 RDTIYDVVERTSKKCFVPLTVGGGVRGVEDINKLLNCGADKVSINTAAVQSPEMIIESSK 118 D + +V+ TS VP+ +GGG+R ++ + KL+N G ++ + TAA++ E E+ K Sbjct: 63 LDAVKSIVQVTS----VPIELGGGIRNIKVVEKLINIGVKRIILGTAALKDKEFTREAIK 118 Query: 119 KFGSQCIVVAIDAKKNGDKWEVFTHGGRNNTNIDAIEFAKKMEDNGAGELLVTSMDRDGT 178 ++G I V IDAK V +G N + I+ IEFAK MED G ++++T + +DGT Sbjct: 119 EYGKS-IAVGIDAKDG----YVAVNGWLNVSKINYIEFAKIMEDMGTEDIILTDISKDGT 173 Query: 179 QIGYDNDLMFKISSTVNIPIIASGGVGNLDHLVDGIRLGNASAVLAASIF 228 G + D++ K+ VN I ASGG+ +LD L+ + A++ +I+ Sbjct: 174 LKGPNFDMLKKLQENVNCNITASGGIKDLDDLIKLKEMNIYGAIVGKAIY 223 Score = 26.6 bits (57), Expect = 5e-04 Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 4/95 (4%) Query: 157 AKKMEDNGAGELLVTSMDRDGTQIG--YDNDLMFKISSTVNIPIIASGGVGNLDHLVDGI 214 AK E++GA + V +D DG G + D + I ++PI GG+ N+ + I Sbjct: 36 AKSFENDGAKYIHV--VDLDGALEGEIINLDAVKSIVQVTSVPIELGGGIRNIKVVEKLI 93 Query: 215 RLGNASAVLAASIFHYGTHSINEAKQYLNSKGIPV 249 +G +L + + K+Y S + + Sbjct: 94 NIGVKRIILGTAALKDKEFTREAIKEYGKSIAVGI 128 Lambda K H 0.317 0.136 0.392 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: 174 Number of extensions: 9 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: 251 Length of database: 239 Length adjustment: 24 Effective length of query: 227 Effective length of database: 215 Effective search space: 48805 Effective search space used: 48805 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