Align phosphoribosylanthranilate isomerase; EC 5.3.1.24 (characterized)
to candidate WP_029132628.1 A3GO_RS0105935 phosphoribosylanthranilate isomerase
Query= CharProtDB::CH_008324 (213 letters) >NCBI__GCF_000428045.1:WP_029132628.1 Length = 210 Score = 212 bits (539), Expect = 5e-60 Identities = 112/214 (52%), Positives = 151/214 (70%), Gaps = 7/214 (3%) Query: 1 MRTRAKICGITRSQDVQAAVSAGADAIGLVFFPPSPRHVSIAQAQALLQHIPAYVQVVGL 60 MRTR KICGITR +D AAV AGADAIGLVF+PPSPR ++ ++A ++Q IP +V VGL Sbjct: 1 MRTRVKICGITRPEDAIAAVRAGADAIGLVFYPPSPRAITASRAAQIIQDIPPFVSTVGL 60 Query: 61 FVNATADQIKSVLDCVALDVLQLHGDETPEQCQEIALQCKRRWYKAIQVKPELDVVDEVQ 120 FVNATAD++ +VL V LD+LQ HGDE P+ C + R + KA++++P++D+ + + Sbjct: 61 FVNATADEVAAVLKTVPLDLLQFHGDEPPDAC----VGHGRPYIKAVRMRPDVDLPELDR 116 Query: 121 RYQAAGASAVLLDAWHPELKGGTGHQFDWSKFP-KLDIPLILAGGLTPENVVDAIQTTHA 179 RYQ+ A +LLD++ P GGTG FDW + P + +ILAGGLTP+NV AIQ Sbjct: 117 RYQS--ALGLLLDSYQPGSPGGTGATFDWGRIPDTMRGRIILAGGLTPQNVAAAIQQVCP 174 Query: 180 FAVDVSGGVEAAKGIKDKQLIERFMQGVQCGSAK 213 +AVDVSGGVE KGIKD++ I FM+GV+ + K Sbjct: 175 YAVDVSGGVEQEKGIKDEEKIRAFMRGVERANRK 208 Lambda K H 0.321 0.135 0.404 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: 169 Number of extensions: 8 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: 213 Length of database: 210 Length adjustment: 21 Effective length of query: 192 Effective length of database: 189 Effective search space: 36288 Effective search space used: 36288 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 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