Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate CCNA_03852 CCNA_03852 phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide isomerase
Query= BRENDA::P16250 (240 letters) >FitnessBrowser__Caulo:CCNA_03852 Length = 244 Score = 149 bits (376), Expect = 5e-41 Identities = 90/245 (36%), Positives = 138/245 (56%), Gaps = 7/245 (2%) Query: 1 MSKLELLPAVDVRDGQAVRLVHGESGTETSYG-SPLEAALAWQRSGAEWLHLVDLDAAF- 58 M+ + L PA+D++DGQ VRL+HG+ T + SP + A + + G WLH+VDL+ A Sbjct: 1 MAPMILYPAIDLKDGQCVRLLHGDMDKATVFNTSPADQAQRFVQDGFSWLHVVDLNGAIE 60 Query: 59 GTGDNRALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVI 118 G N A + ++ +++ I V+L GGIR + + A + G +RV LGT A+ PE V K Sbjct: 61 GKSVNTAAVEQILESISIPVQLGGGIRTLEGVEAWIEAGVSRVILGTVAVHDPELVKKAA 120 Query: 119 AEHGDKIAVGLDVRGTTLRGRGWTRDGGDLYETLD---RLNKEGCARYVVTDIAKDGTLQ 175 ++IAV +DVR + GWT G +D R G A ++TDI++DG L Sbjct: 121 RLWPEQIAVAVDVRDGKVAVDGWT--GLSDLSAIDLSRRFEDAGVAALIITDISRDGALT 178 Query: 176 GPNLELLKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEA 235 G N+E + + A PV+ASGGV+++ D+ + + GAI+G++LYA EA Sbjct: 179 GVNVEGVGELADAVSIPVIASGGVAAVADIERLKARQGVEIAGAILGRSLYAGTIKPSEA 238 Query: 236 LEATS 240 L A + Sbjct: 239 LIAAA 243 Lambda K H 0.315 0.133 0.385 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: 168 Number of extensions: 15 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: 240 Length of database: 244 Length adjustment: 23 Effective length of query: 217 Effective length of database: 221 Effective search space: 47957 Effective search space used: 47957 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 (22.0 bits) S2: 46 (22.3 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