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 WP_043769570.1 U743_RS15675 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= curated2:A9GBI6 (270 letters) >NCBI__GCF_000733765.1:WP_043769570.1 Length = 243 Score = 99.4 bits (246), Expect = 7e-26 Identities = 80/255 (31%), Positives = 127/255 (49%), Gaps = 25/255 (9%) Query: 6 IIPCLDVKDGRVVKGVRFVGLRD----AGDPVEAARRYDAEGADEITFLDITASHEKRGI 61 +IP +D+K+G+ V+ +R + D + DPV ARR+ GA+ + +D+ + R + Sbjct: 3 LIPAIDIKNGQCVR-LRQGKMDDVTVFSEDPVAVARRWAEAGAERLHIVDLDGAATGRPV 61 Query: 62 ILDVVARTAEVLFT-PLTVGGGVKSEQDIKALLDAGADKVAINTAAVNDPDLVRRAADRW 120 +++ R E + VGGG++ E+ ++ LDAGA V I T AV P +R + Sbjct: 62 HAELIQRICEANPNLAVQVGGGIRDEEAVQGYLDAGAQWVIIGTRAVTAPHFLRDLCVEY 121 Query: 121 GAQAIVVAIDARRIADPSRVA---WTVVTHGGRRDTGRDAVAWAEEIARAGAGELLVTSM 177 + IVV +DAR RVA W+ ++H + A++ G ++ T + Sbjct: 122 -PRHIVVGLDAR----DGRVAVDGWSKLSH-------HTVLELAQQFEEDGVEAIVYTDI 169 Query: 178 DRDGTRDGYDLLLTAAIARAVPVPVIASGGVGTLDHLRA--GLVEGGADAALAASIFHDA 235 RDG G ++ T +A + PVIASGGV T+D LRA + E G A+ + Sbjct: 170 GRDGMMKGVNVEATRELAAQIRTPVIASGGVSTMDDLRALHAVEEDGVVGAIIGRALY-- 227 Query: 236 EYTIGEAKAYLEAAG 250 E TI +A E AG Sbjct: 228 EGTIDFKQAIEEMAG 242 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: 171 Number of extensions: 11 Number of successful extensions: 5 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: 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