Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_013076130.1 BTUS_RS10915 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= BRENDA::P16250 (240 letters) >NCBI__GCF_000092905.1:WP_013076130.1 Length = 281 Score = 172 bits (435), Expect = 8e-48 Identities = 99/237 (41%), Positives = 139/237 (58%), Gaps = 3/237 (1%) Query: 2 SKLELLPAVDVRDGQAVRLVHGESGTETSYGS-PLEAALAWQRSGAEWLHLVDLDAAF-G 59 ++ +L PA+D+ DG+AVRL G+ G T YG P+ A W+ GA WLH+VDLD A G Sbjct: 5 AEFQLYPAIDLSDGRAVRLRQGDYGQMTVYGDDPVAVARRWRDEGAGWLHVVDLDGAKEG 64 Query: 60 TGDNRALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIA 119 + LI + +A + V++ GGIRD ++L A + G R LGTAALE P W+ +V+A Sbjct: 65 HPVHLPLIGRMVEAAGLPVQVGGGIRDGESLRALFSLGVARCVLGTAALENPVWMKEVLA 124 Query: 120 EHGDKIAVGLDVRGTTLRGRGWTRDGGDLYETLDRLNKE-GCARYVVTDIAKDGTLQGPN 178 E+G++I VGLD R + RGW ++ G L R KE G R + TDI +DG + GP Sbjct: 125 EYGERIVVGLDARDGKVAVRGWLQNTGVAAVELGRRLKEWGARRALFTDIRRDGAMAGPG 184 Query: 179 LELLKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEA 235 + T V+ASGGV L D++ + L GV GA+ G+ALY +L+EA Sbjct: 185 GREAAELAEETGLLVIASGGVRHLGDIQRLYALRHRGVAGAVAGRALYTGDLSLKEA 241 Lambda K H 0.315 0.133 0.385 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: 242 Number of extensions: 19 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: 240 Length of database: 281 Length adjustment: 24 Effective length of query: 216 Effective length of database: 257 Effective search space: 55512 Effective search space used: 55512 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: 42 (22.0 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