Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_058929461.1 AU252_RS03030 bifunctional 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase/phosphoribosylanthranilate isomerase PriA
Query= BRENDA::P16250 (240 letters) >NCBI__GCF_001484605.1:WP_058929461.1 Length = 248 Score = 338 bits (866), Expect = 8e-98 Identities = 167/234 (71%), Positives = 192/234 (82%) Query: 4 LELLPAVDVRDGQAVRLVHGESGTETSYGSPLEAALAWQRSGAEWLHLVDLDAAFGTGDN 63 LELLPAVDV +GQAVRLV GE+G+ETSYG+PLEAAL WQ GAEW+HLVDLDAAFG G N Sbjct: 10 LELLPAVDVVNGQAVRLVQGEAGSETSYGTPLEAALNWQEQGAEWVHLVDLDAAFGRGSN 69 Query: 64 RALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHGD 123 L+ EV +DIKVELSGG+RDD++L AALA G RVNLGTAALE PEW I GD Sbjct: 70 AELLREVVGRLDIKVELSGGLRDDESLEAALALGVARVNLGTAALENPEWTRSAIDRFGD 129 Query: 124 KIAVGLDVRGTTLRGRGWTRDGGDLYETLDRLNKEGCARYVVTDIAKDGTLQGPNLELLK 183 +IAVGLDVRGTTL GRGWT++GGDL+E L RL + GC+RYVVTD+ KDGTLQGPN+ELL+ Sbjct: 130 RIAVGLDVRGTTLAGRGWTKEGGDLWEVLGRLEEAGCSRYVVTDVTKDGTLQGPNVELLR 189 Query: 184 NVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEALE 237 + T +PVVASGG+SSLDDL+ + LVP GVEGAIVGKALYA AFTL EAL+ Sbjct: 190 QMVEKTGKPVVASGGISSLDDLKVLRSLVPLGVEGAIVGKALYAGAFTLPEALD 243 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: 253 Number of extensions: 9 Number of successful extensions: 2 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: 248 Length adjustment: 24 Effective length of query: 216 Effective length of database: 224 Effective search space: 48384 Effective search space used: 48384 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