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 RR42_RS18890 RR42_RS18890 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= curated2:Q7W2X9 (269 letters) >FitnessBrowser__Cup4G11:RR42_RS18890 Length = 248 Score = 103 bits (256), Expect = 5e-27 Identities = 72/234 (30%), Positives = 115/234 (49%), Gaps = 25/234 (10%) Query: 18 IIPCLDVTAGRVVK---GVNFVNLTDAGDPVEIARRYNEQGADELTFLDITATSDGHDLI 74 +IP +D+ G+ V+ G + DP +AR + EQGA L +D+ G Sbjct: 3 LIPAIDLKDGQCVRLKQGDMDQATVFSEDPAAMARHWVEQGARRLHLVDLNGAFVGKPRN 62 Query: 75 LPIIEQVASQVF--IPLTVGGGVRQVSDVQRLLNAGADKISINSAAVANPELVRAAADYH 132 I+ + ++V IP+ +GGG+R ++ ++R L+ G + I +AAV NP ++ A Sbjct: 63 EAAIKAIIAEVGDEIPIQLGGGIRDLNTIERWLDGGLSYVIIGTAAVKNPGFLKDACTAF 122 Query: 133 GSQCIVVAIDARRSSAEGEPARWEVFTHGGRKATGLDAVAWARRMAAYGAGEILLTSMDR 192 G I+V +DAR +V T G K TG + AR+ YG I+ T + R Sbjct: 123 GGH-IIVGLDAREG---------KVATDGWSKLTGHEVADLARKYEDYGVEAIIYTDIGR 172 Query: 193 DGTKSGFDLELTRAVSDAVPVPVIASGGVGNLQHL----------ADGVTTGRA 236 DG G +++ T ++ + +PVIASGG+ NL + +GV GRA Sbjct: 173 DGMLQGINIDATVKLAQSATIPVIASGGLSNLADIERLCSVQKDGVEGVICGRA 226 Lambda K H 0.319 0.133 0.382 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: 189 Number of extensions: 14 Number of successful extensions: 4 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: 269 Length of database: 248 Length adjustment: 24 Effective length of query: 245 Effective length of database: 224 Effective search space: 54880 Effective search space used: 54880 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 (21.8 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