Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate Dsui_1417 Dsui_1417 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
Query= BRENDA::P16250 (240 letters) >FitnessBrowser__PS:Dsui_1417 Length = 246 Score = 145 bits (366), Expect = 7e-40 Identities = 90/240 (37%), Positives = 129/240 (53%), Gaps = 9/240 (3%) Query: 6 LLPAVDVRDGQAVRLVHGESGTETSYG-SPLEAALAWQRSGAEWLHLVDLDAAFG----- 59 ++PA+D++DGQ VRL G T + SP E A W GA LHLVDL+ AF Sbjct: 3 IIPAIDLKDGQCVRLKQGLMEEATVFSESPAEQARHWLDQGARRLHLVDLNGAFAGQPKN 62 Query: 60 TGDNRALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIA 119 G +A++ EV +I V+L GGIRD DT+ L G T V +GTAA++ P ++ Sbjct: 63 QGAIKAILKEVGD--EIPVQLGGGIRDLDTIERCLDAGLTYVIIGTAAVKNPGFLHDACV 120 Query: 120 EHGDKIAVGLDVRGTTLRGRGWTR-DGGDLYETLDRLNKEGCARYVVTDIAKDGTLQGPN 178 I VGLD + + GW++ G D+ + + G + TDI +DG L G N Sbjct: 121 AFPGHIIVGLDAKDGKVAVDGWSKLTGHDVIDLAKKYEDYGVESIIYTDIGRDGMLSGIN 180 Query: 179 LELLKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEALEA 238 +E + A PV+ASGG+S+LDD+R + + GV G I G+A+Y + + A EA Sbjct: 181 IEATVKLAQALKIPVIASGGLSNLDDIRKLCEVEGEGVVGTIAGRAIYDGSLDFKAAQEA 240 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: 166 Number of extensions: 12 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: 240 Length of database: 246 Length adjustment: 23 Effective length of query: 217 Effective length of database: 223 Effective search space: 48391 Effective search space used: 48391 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