Align phosphoribosylanthranilate isomerase; EC 5.3.1.24 (characterized)
to candidate WP_086508779.1 BZY95_RS04470 phosphoribosylanthranilate isomerase
Query= CharProtDB::CH_008324 (213 letters) >NCBI__GCF_002151265.1:WP_086508779.1 Length = 217 Score = 176 bits (446), Expect = 3e-49 Identities = 101/207 (48%), Positives = 129/207 (62%), Gaps = 9/207 (4%) Query: 2 RTRAKICGITRSQDVQAAVSAGADAIGLVFFPPSPRHVSIAQAQALLQHIPAYVQVVGLF 61 RTR K CG++R QDV AV+AGADA+G V +P S R V A+ L +PA+V VGLF Sbjct: 10 RTRIKFCGLSREQDVADAVAAGADALGFVLWPGSKRCVDEARLATLAAQVPAFVTRVGLF 69 Query: 62 VNATADQIKSVLDCVALDVLQLHGDETPEQCQEIALQCKRRWYKAIQVKPELDVVDEVQR 121 V+ + I + LD+LQ HGDETP C R W KA++++ +LD+ + Sbjct: 70 VDQEPELIARSAE--HLDLLQFHGDETPAFCAGFG----RPWIKALRMRDDLDLHAAAEA 123 Query: 122 YQAAGASAVLLDAWHPELKGGTGHQFDWSKFP-KLDIPLILAGGLTPENVVDAIQTTHAF 180 Y AGA A+LLDA+ P + GGTG FDWS+ P L P+ILAGGL P+NV AI+ F Sbjct: 124 Y--AGAQALLLDAYRPGVPGGTGETFDWSRIPANLAKPVILAGGLGPDNVAQAIERVRPF 181 Query: 181 AVDVSGGVEAAKGIKDKQLIERFMQGV 207 AVDVSGGVEAA G KD+ L+ F V Sbjct: 182 AVDVSGGVEAAPGRKDRGLLAAFAAAV 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: 161 Number of extensions: 11 Number of successful extensions: 5 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: 217 Length adjustment: 22 Effective length of query: 191 Effective length of database: 195 Effective search space: 37245 Effective search space used: 37245 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