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 350907 BT1379 phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (NCBI ptt file)
Query= curated2:Q12UY6 (273 letters) >FitnessBrowser__Btheta:350907 Length = 239 Score = 70.5 bits (171), Expect = 3e-17 Identities = 60/263 (22%), Positives = 116/263 (44%), Gaps = 37/263 (14%) Query: 6 IIPCLDVTLDASGGTVVKGVEFVDLKKA--GDPVDLAKRYNEQGADELVFLDITASHEGR 63 IIP +D+ G V D KK +PV++AK + G L +D+ + Sbjct: 4 IIPAIDII---DGKCVRLSQGDYDSKKVYNENPVEVAKEFEANGVRRLHVVDLDGAASHH 60 Query: 64 STMIDVIERTANEVFIPLTVGGGINSVEDVRQILRAGADKVSVNTAAVKNPEFIREASNI 123 V+E+ A + + GGG+ S ED++ +GA V+ + AVK+PE + Sbjct: 61 VVNHRVLEQIATRTSLIVDFGGGVKSDEDLKIAFESGAQMVTGGSVAVKDPELFCHWLEV 120 Query: 124 FGSQCIVTAIDCKRNLDVENNQDKTILELEDGTLAWYEVVIYGGREPTGLDTVQWAKKVE 183 +GS+ I+ D K +++ + G ++ + + + + Sbjct: 121 YGSEKIILGADVKE----------------------HKIAVNGWKDESACELFPFLEDYI 158 Query: 184 ELGSGEILLTSMNRDGTYDGFDIPITKKLSEEL-DIPIIASGGVGNPEHMYKGFVDGKAD 242 G +++ T ++ DG G I + K++ E+ ++ ++ASGGV N + + + Sbjct: 159 NKGIQKVICTDISCDGMLKGPSIDLYKEMLEKFPNLYLMASGGVSNVDD-----IIALNE 213 Query: 243 AGLAASIF----HFGEYTVRDVK 261 AG+ IF + G T++D++ Sbjct: 214 AGVPGVIFGKALYEGHITLKDLR 236 Lambda K H 0.317 0.137 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: 192 Number of extensions: 6 Number of successful extensions: 2 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: 273 Length of database: 239 Length adjustment: 24 Effective length of query: 249 Effective length of database: 215 Effective search space: 53535 Effective search space used: 53535 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: 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