Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate GFF3066 HP15_3010 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= BRENDA::P16250 (240 letters) >FitnessBrowser__Marino:GFF3066 Length = 245 Score = 143 bits (360), Expect = 4e-39 Identities = 83/234 (35%), Positives = 131/234 (55%), Gaps = 4/234 (1%) Query: 6 LLPAVDVRDGQAVRLVHGESGTETSYGS-PLEAALAWQRSGAEWLHLVDLDAAF-GTGDN 63 ++PA+D++DG+ VRL G T +G P++ A W +GA LHLVDL+ AF G N Sbjct: 3 IIPAIDLKDGKCVRLRQGRMDDSTVFGDDPVDMATRWVEAGARRLHLVDLNGAFAGEPVN 62 Query: 64 RALIAEVAQAM-DIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHG 122 ++ +A+ D+ +++ GGIR +T+ A L G V +GT A++ PE+V ++ + Sbjct: 63 GEIVQAIARKYPDLPIQIGGGIRSAETIEAYLKAGVQWVIIGTKAVKEPEFVTEMCKKFP 122 Query: 123 DKIAVGLDVRGTTLRGRGWTRDGGDLYETL-DRLNKEGCARYVVTDIAKDGTLQGPNLEL 181 I VGLD + + GW + L R +G V TDI++DG +QG N+E Sbjct: 123 GHIIVGLDAKDGRVATDGWAEVSEVMATDLAKRFANDGVDAIVYTDISRDGMMQGVNVEA 182 Query: 182 LKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEA 235 + PV+ASGGV+++DDL+ +A + G+ GAI G+A+Y + EA Sbjct: 183 TAALAEEGGIPVIASGGVTNMDDLKRLATVADKGILGAITGRAIYEGTLDVAEA 236 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: 180 Number of extensions: 14 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: 245 Length adjustment: 23 Effective length of query: 217 Effective length of database: 222 Effective search space: 48174 Effective search space used: 48174 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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