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_017600195.1 D471_RS0119660 bifunctional 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase/phosphoribosylanthranilate isomerase PriA
Query= curated2:A2BPR2 (256 letters) >NCBI__GCF_000341125.1:WP_017600195.1 Length = 250 Score = 92.4 bits (228), Expect = 8e-24 Identities = 72/246 (29%), Positives = 123/246 (50%), Gaps = 22/246 (8%) Query: 3 ALRLIPCLDVAHGRVVKGVNFVNLRDS--GDPVELACRYSDEGADELVFLDIRASV---E 57 AL L+P +DVA G+ V+ V GDP+ A R+ + GA+ + +D+ A+ Sbjct: 9 ALELLPAVDVAGGQAVQLVQGEAGSGGRYGDPLTAATRWQEAGAEWIHLVDLDAAFGRGH 68 Query: 58 NRNTLVDLVSRTAKSVKIPFTVGGGIDSVSSINDLLRAGADKVSLNSSAVRNPDLISKSS 117 NR+ L D+V R V++ GGI S+ L G +V++ ++A+ NP+ +K Sbjct: 69 NRDLLRDIVGRLDVKVEM----SGGIRDDESLAAALATGCTRVNIGTAALENPEWCAKII 124 Query: 118 REFGNQCIVIAIDARRKVNKFGEWEVYVKGGRENTGIDVLSWAKKVEELGAGEILLTSMD 177 + G++ I I +D R W G D+ + +++E G ++T ++ Sbjct: 125 AQHGDR-IAIGLDVRGTTLAARGWT--------REGGDLFTTLERLESEGCARYVVTDVN 175 Query: 178 GDGTQNGYDLNLTESVANIVDIPVIASGGAGSLED---IFDVFKEGRASAALLASLLHDK 234 DGT G +L+L +V D PV+ASGG SL+D I + EG A++ + L++ Sbjct: 176 KDGTLKGPNLDLLRTVCARTDKPVVASGGVSSLDDLSAIATLVPEG-VEGAIMGTALYEG 234 Query: 235 KLTLKE 240 TL++ Sbjct: 235 AFTLED 240 Lambda K H 0.316 0.136 0.380 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: 193 Number of extensions: 18 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: 256 Length of database: 250 Length adjustment: 24 Effective length of query: 232 Effective length of database: 226 Effective search space: 52432 Effective search space used: 52432 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