Align N-(5'-phosphoribosyl)anthranilate isomerase; PRAI; EC 5.3.1.24 (uncharacterized)
to candidate 8501005 DvMF_1742 Phosphoribosylanthranilate isomerase (RefSeq)
Query= curated2:B8J162 (211 letters) >FitnessBrowser__Miya:8501005 Length = 225 Score = 216 bits (551), Expect = 2e-61 Identities = 112/205 (54%), Positives = 133/205 (64%), Gaps = 6/205 (2%) Query: 1 MLIKVCGLTRQADVDLAASFGASMCGFIFHPVSPRCVSPVQAASLESGSMLRVGVFVEQD 60 +L+KVCGLTRQ D D A G +CGFIFHP SPR V+P AA L S M RVGVFV+Q Sbjct: 16 LLVKVCGLTRQQDADACAEAGVDLCGFIFHPASPRGVTPAVAAGLHSHGMARVGVFVKQS 75 Query: 61 AEEICRIMAEARLDMAQLHGRQDAACARAVGAQRVIRVIWPARYCHRALLYNELQNHADA 120 A+E+ +M ARLD AQLHG QDAA VG +RVIR WP R+ R+ L EL A Sbjct: 76 ADEVLAVMDAARLDFAQLHGGQDAAFCDRVGPERVIRAAWPQRHADRSALQAELAGLAPH 135 Query: 121 CACYLLDAGLAGGGSGVRLDWEDLNHLPSPRPWLLAGGLSAENVGLALSRCSPD------ 174 C+LLDAG +GGG G +DW L L PWLLAGGL+ +NV A++ C Sbjct: 136 VRCFLLDAGTSGGGHGATMDWSALRGLAPGAPWLLAGGLTPDNVASAVAACGGHDPGALI 195 Query: 175 GVDFNSGVEDAPGQKNAQKLAAALA 199 GVD NSGVE APGQK+A ++AAALA Sbjct: 196 GVDLNSGVESAPGQKDATRVAAALA 220 Lambda K H 0.322 0.135 0.418 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: 152 Number of extensions: 5 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: 211 Length of database: 225 Length adjustment: 22 Effective length of query: 189 Effective length of database: 203 Effective search space: 38367 Effective search space used: 38367 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 (21.9 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Apr 09 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