Align N-(5'-phosphoribosyl)anthranilate isomerase; PRAI; EC 5.3.1.24 (uncharacterized)
to candidate WP_010932400.1 AYT24_RS03345 phosphoribosylanthranilate isomerase
Query= curated2:B3QMF2 (221 letters) >NCBI__GCF_000006985.1:WP_010932400.1 Length = 221 Score = 328 bits (841), Expect = 5e-95 Identities = 156/218 (71%), Positives = 184/218 (84%) Query: 1 MTRIKICGITRAEDALTAALAGADALGFNFSKKSPRLVSPDTAREIIAALPPLVAPVGIF 60 MT+IKICGITRA+DAL AALAGADALGFNFS+KSPR + +TAR IIA LPPLV PVG+F Sbjct: 1 MTKIKICGITRAQDALEAALAGADALGFNFSRKSPRRIDAETARSIIAGLPPLVTPVGVF 60 Query: 61 VEQSAEEINELCRYCGLQIAQLHSDEYGAEATMRIHGTKVIRVFRPGPGFSVNEVRTYAK 120 VEQS EEIN++CR+CGL +AQLHSD+Y AE T++I G +VIRVFRP PGF V++VR + + Sbjct: 61 VEQSPEEINDICRHCGLLVAQLHSDDYDAEKTLQIKGVRVIRVFRPSPGFEVSQVRKFTE 120 Query: 121 QTGCRGFLFDAFSPEMAGGTGKTIESSTASMLFEQTRDIGWALLAGGLNPENVADAVRLI 180 +TGCR FLFDA+SP MAGGTG++IE+ TA LF++TRD WALLAGGL PENV DAV LI Sbjct: 121 KTGCRSFLFDAYSPAMAGGTGQSIEAQTAGSLFDETRDFSWALLAGGLKPENVGDAVTLI 180 Query: 181 NPWGVDTASGVESAPGIKDARKITSFIQAVREVDRMLT 218 PWGVDTASGVES PGIKDA KI F++AVR+ DR LT Sbjct: 181 RPWGVDTASGVESGPGIKDALKIRQFVEAVRKADRSLT 218 Lambda K H 0.319 0.135 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: 202 Number of extensions: 4 Number of successful extensions: 1 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: 221 Length of database: 221 Length adjustment: 22 Effective length of query: 199 Effective length of database: 199 Effective search space: 39601 Effective search space used: 39601 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 (21.8 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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