Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_041777864.1 BIND_RS01230 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= BRENDA::P16250 (240 letters) >NCBI__GCF_000019845.1:WP_041777864.1 Length = 245 Score = 137 bits (345), Expect = 2e-37 Identities = 84/229 (36%), Positives = 124/229 (54%), Gaps = 3/229 (1%) Query: 1 MSKLELLPAVDVRDGQAVRLVHGESGTETSYGS-PLEAALAWQRSGAEWLHLVDLDAAF- 58 M+ + L PA+D+++G VRL+ G+ T + P A A++ G LH+VDLD AF Sbjct: 1 MAPMILYPAIDLKEGHCVRLLQGDMQKATIFNDDPAAQAAAFEAQGFTALHVVDLDGAFA 60 Query: 59 GTGDNRALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVI 118 G N A + + + + V+L GGIRD+ T+ A L G RV +GTAA+ P+ V + Sbjct: 61 GKPMNAAAVDAILARVKMSVQLGGGIRDEATIEAWLGKGIARVIIGTAAVRDPDLVRRAA 120 Query: 119 AEHGDKIAVGLDVRGTTLRGRGWTRDGG-DLYETLDRLNKEGCARYVVTDIAKDGTLQGP 177 A KIAVG+D + + GW + E + G A + TDIA+DG L G Sbjct: 121 ARFPGKIAVGIDAKDGFVAVEGWAKTAQLSAVELGKKFEDAGVAALIYTDIARDGGLTGL 180 Query: 178 NLELLKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALY 226 N++ + A PV+ASGG++SL D+ + A + GAI G+ALY Sbjct: 181 NIDATLALAKAVHIPVIASGGLASLADIERLTAPDCAILAGAISGRALY 229 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: 142 Number of extensions: 12 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: 240 Length of database: 245 Length adjustment: 23 Effective length of query: 217 Effective length of database: 222 Effective search space: 48174 Effective search space used: 48174 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: 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