Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate GFF911 PGA1_c09270 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase HisA
Query= BRENDA::P16250 (240 letters) >FitnessBrowser__Phaeo:GFF911 Length = 240 Score = 159 bits (401), Expect = 6e-44 Identities = 94/235 (40%), Positives = 134/235 (57%), Gaps = 4/235 (1%) Query: 6 LLPAVDVRDGQAVRLVHGESGTETSYGS-PLEAALAWQRSGAEWLHLVDLDAAF-GTGDN 63 L PA+D++DGQAVRL+HG+ T + P AL + +G +WLHLVDL+ AF G N Sbjct: 3 LYPAIDLKDGQAVRLLHGDMEKTTVFNDDPAAQALEFVEAGCDWLHLVDLNGAFAGEPVN 62 Query: 64 RALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHGD 123 A + ++ + + +L GGIRD T+ + G RV LGT A+E P+ V + Sbjct: 63 AAPVEKILKRCKVPAQLGGGIRDMATIERWIDKGLARVILGTVAVENPDLVREAARAFPG 122 Query: 124 KIAVGLDVRGTTLRGRGWTRDGGDLYETLDR-LNKEGCARYVVTDIAKDGTLQGPNLELL 182 K+AVG+D R + +GW + + L + G A + TDI +DG ++GPN+E Sbjct: 123 KVAVGIDARNGRVATKGWAEETDVMVTDLAKSFEDAGVAAIIYTDILRDGAMKGPNVEAT 182 Query: 183 KNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEALE 237 + A PV+ASGGVSSL DL+A+ A + GAI G+ALY A L EAL+ Sbjct: 183 AALANAVSIPVIASGGVSSLADLQALKS-CGAPLNGAISGRALYDGAIDLGEALK 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: 159 Number of extensions: 12 Number of successful extensions: 6 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: 240 Length adjustment: 23 Effective length of query: 217 Effective length of database: 217 Effective search space: 47089 Effective search space used: 47089 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