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 8502414 DvMF_3120 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq)
Query= curated2:A9GBI6 (270 letters) >FitnessBrowser__Miya:8502414 Length = 243 Score = 101 bits (251), Expect = 2e-26 Identities = 68/216 (31%), Positives = 107/216 (49%), Gaps = 16/216 (7%) Query: 6 IIPCLDVKDGRVVKGVRFVGLRDA-----GDPVEAARRYDAEGADEITFLDITASHEKRG 60 + P +D+KDGR V+ + G DA DP AR + +GA + +D+ + Sbjct: 3 LFPAVDIKDGRCVRLRQ--GRADAETVFSDDPAAMARHWQDQGAKWLHVIDLDGAFSGMP 60 Query: 61 IILDVVARTAEVLFTPLTVGGGVKSEQDIKALLDAGADKVAINTAAVNDPDLVRRAADRW 120 +++ R L P+ +GGG++ E KA LDAG +++ I T A+ +PDL R + Sbjct: 61 ANFELIRRICADLSVPVQLGGGIRDEATAKAYLDAGVERLIIGTVALEEPDLYARLCATF 120 Query: 121 GAQAIVVAIDARRIADPSRVAWTVVTHGGRRDTGRDAVAWAEEIARAGAGELLVTSMDRD 180 + I V++DA + T G D+G + AG ++ T +DRD Sbjct: 121 PGR-IGVSLDAE--------GGRLKTKGWVADSGLTVDDVLPRLLAAGTAFVIYTDIDRD 171 Query: 181 GTRDGYDLLLTAAIARAVPVPVIASGGVGTLDHLRA 216 G + G +L +A PVPVIA+GGV TL+ +RA Sbjct: 172 GMQTGVNLSALERLAGMCPVPVIAAGGVATLEDVRA 207 Score = 32.0 bits (71), Expect = 1e-05 Identities = 34/121 (28%), Positives = 53/121 (43%), Gaps = 9/121 (7%) Query: 5 RIIPCLDVKDGRV-VKGVRFVGLRDAGDPVE-AARRYDAEGADEITFLDITASHEKRGII 62 RI LD + GR+ KG + D+G V+ R A G + + DI + G+ Sbjct: 123 RIGVSLDAEGGRLKTKG----WVADSGLTVDDVLPRLLAAGTAFVIYTDIDRDGMQTGVN 178 Query: 63 LDVVARTAEVLFTPLTVGGGVKSEQDIKALLD---AGADKVAINTAAVNDPDLVRRAADR 119 L + R A + P+ GGV + +D++AL + + AI A+ L AA Sbjct: 179 LSALERLAGMCPVPVIAAGGVATLEDVRALYPMTLTSSVEGAITGRAIYTGTLDLHAAME 238 Query: 120 W 120 W Sbjct: 239 W 239 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: 146 Number of extensions: 7 Number of successful extensions: 4 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: 243 Length adjustment: 24 Effective length of query: 246 Effective length of database: 219 Effective search space: 53874 Effective search space used: 53874 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