Align N-(5'-phosphoribosyl)anthranilate isomerase; PRAI; EC 5.3.1.24 (uncharacterized)
to candidate WP_013451105.1 CALNI_RS10855 phosphoribosylanthranilate isomerase
Query= curated2:O67853 (204 letters) >NCBI__GCF_000183405.1:WP_013451105.1 Length = 175 Score = 89.7 bits (221), Expect = 3e-23 Identities = 69/199 (34%), Positives = 99/199 (49%), Gaps = 26/199 (13%) Query: 4 VKICGITNLEDALFCAKEGADYIGVITYPKSPRYTSKEKRLEIIKALEGLNVKKVAVVVN 63 VK+CGIT E + + G D IGV+ YPKS R+ K+K +E+ + G K V V Sbjct: 3 VKVCGITQKEYIDWAVELGFDAIGVVFYPKSKRFVDKDKGIELAEYSRG---KISTVAVG 59 Query: 64 EPYEFIKELLDEGFDLIQLHGDEDIELGKRVGLDKVIKVFRVKEEIPKVGEWEKAYAILL 123 YE IK++ D FD Q+ +DK + ++ ++E+ K L Sbjct: 60 IIYEEIKDVKDY-FDYYQI---------SEYMVDKKL-IYSIEEKPDKEAN--------L 100 Query: 124 DTFSKEAYGGTGKTFNWEIAKKLVEEGHKVFLSGGLNPENVKEGIEFVKPYGVDVSSGVE 183 F K GG EI + E HK ++GGLN +NV + ++ P+GVDVSSGVE Sbjct: 101 YIFDKSKGGGIFS----EIPEWFYEIKHKTIIAGGLNAKNVVDLVKTYSPFGVDVSSGVE 156 Query: 184 KEKGKKDFKKVREFIKRTK 202 G K + +R+FIK K Sbjct: 157 ITPGVKSKELMRDFIKNLK 175 Lambda K H 0.315 0.139 0.393 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: 127 Number of extensions: 8 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: 204 Length of database: 175 Length adjustment: 20 Effective length of query: 184 Effective length of database: 155 Effective search space: 28520 Effective search space used: 28520 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 (21.9 bits) S2: 44 (21.6 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