Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate Ga0059261_1047 Ga0059261_1047 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (EC 5.3.1.16)
Query= BRENDA::P16250 (240 letters) >FitnessBrowser__Korea:Ga0059261_1047 Length = 242 Score = 152 bits (384), Expect = 6e-42 Identities = 92/238 (38%), Positives = 134/238 (56%), Gaps = 5/238 (2%) Query: 6 LLPAVDVRDGQAVRLVHGESGTETSYG-SPLEAALAWQRSGAEWLHLVDLDAAF-GTGDN 63 + PA+D++ GQ VRL G+ T YG +P A A+ ++GA LH+VDLDAAF G N Sbjct: 3 VFPAIDLKAGQVVRLAEGDMTRATVYGENPAAQAEAFAKAGATHLHVVDLDAAFAGESIN 62 Query: 64 RALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHGD 123 +A + KV+L GGIR+ ++ + G +RV +GTAALE P++V + A H Sbjct: 63 GGAVAAILARFPGKVQLGGGIRNRASVERWIDMGVSRVVIGTAALEDPDFVREAAAAHPG 122 Query: 124 KIAVGLDVRGTTLRGRGWTR-DGGDLYETLDRLNKEGCARYVVTDIAKDGTLQGPNLELL 182 +I V +D R + +GW + E R G A + TD+ +DG L+G N+E Sbjct: 123 QIVVAVDARDGFVATKGWADVSTVSIAELGHRFEDAGVAALLFTDVGRDGLLKGCNVEAT 182 Query: 183 KNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEALEATS 240 + A PV+ASGGV+ + D+ A+AG G+EG I G+ALY L EAL+A + Sbjct: 183 AALAAEVSIPVIASGGVADISDIHALAG--KPGIEGVITGRALYDGRLDLAEALKAAA 238 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: 158 Number of extensions: 9 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: 242 Length adjustment: 23 Effective length of query: 217 Effective length of database: 219 Effective search space: 47523 Effective search space used: 47523 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