Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate WP_057506753.1 ABB28_RS00555 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q2JK82 (261 letters) >NCBI__GCF_001431535.1:WP_057506753.1 Length = 258 Score = 105 bits (263), Expect = 7e-28 Identities = 76/244 (31%), Positives = 121/244 (49%), Gaps = 15/244 (6%) Query: 10 VIPAIDLLQGRAVRLYQ-GDYAQAEQVADDPIQQAEAWAAQGAPRLHVVDLDGAKSGDPV 68 +IP +D+ GR V+ + D+ +A+ ++ + QGA L D+ + G V Sbjct: 6 IIPCLDVRDGRVVKGVRFRDHVDMGDIAELALRYRD----QGADELVFYDIGASPDGRSV 61 Query: 69 NLPIIERIVRSLAIPVQVGGGIRSLERARQLLDLGVDRVIVGTLAVEDPDTLEAMTQAFP 128 ++ IERI R + IP V GGI +E AR++L G D++ + + A+ P+ + + AF Sbjct: 62 DVEWIERIARLIDIPFCVAGGISDVETARRVLHAGADKISINSPALGRPELITELADAFG 121 Query: 129 GR-VWVGIDA---RQGQVATRGWLS------TTPLRAPELVQRVQAQGAAGIIYTDISRD 178 + V VGID+ GQ R + +R + V+ VQ +GA I+ + D Sbjct: 122 VQCVVVGIDSVREADGQWRVRRFTGDPSKTQAVAVRTLDWVREVQQRGAGEIVLNCMDSD 181 Query: 179 GTLAGPNLEQLRQILAVSQVPVIASGGIGSLTDLLALLSLPRLTGAILGKALYSGAISLQ 238 G G ++EQLR A VP+IASGG GS + + GA+ +SGAI++ Sbjct: 182 GVRRGYDVEQLRHARAACHVPLIASGGAGSREHFAQVFDQADVDGALAASVFHSGAIAIP 241 Query: 239 EALR 242 E R Sbjct: 242 ELKR 245 Lambda K H 0.319 0.137 0.400 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: 182 Number of extensions: 14 Number of successful extensions: 3 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: 261 Length of database: 258 Length adjustment: 24 Effective length of query: 237 Effective length of database: 234 Effective search space: 55458 Effective search space used: 55458 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 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