Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_017550016.1 C792_RS0113615 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= BRENDA::P16250 (240 letters) >NCBI__GCF_000330705.1:WP_017550016.1 Length = 233 Score = 105 bits (263), Expect = 6e-28 Identities = 70/231 (30%), Positives = 115/231 (49%), Gaps = 7/231 (3%) Query: 4 LELLPAVDVRDGQAVRLVHGESGTETSYGSPLEAALAWQRSGAEW--LHLVDLDAAFGTG 61 + ++PA+D+ DG+ VRL G+ T+ E A+ + + +H+VDL A Sbjct: 1 MNIIPAIDIIDGRNVRLKQGDYDQRTAMKRTPEEAIRFYSGFRQVGRIHIVDLMGALKQD 60 Query: 62 DNRALIAEVAQAM-DIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAE 120 + + E ++ D+ +++ GG+R+ +T+ G LGT A+ +W+ + + E Sbjct: 61 AQESTVIEKLKSQTDLPLQIGGGLRNMETIRQYDRIGIDYFILGTKAILDTDWLKEAVRE 120 Query: 121 HGDKIAVGLDVRGTTLRGRGWTRDGG-DLYETLDRLNKEGCARYVVTDIAKDGTLQGPNL 179 +I VG D R + GWT + + E + + A + TDI KDG QGPN Sbjct: 121 FPGRIFVGTDARENDIYVNGWTENSDITIDEYIREIEGLDIAGIIYTDINKDGMNQGPNF 180 Query: 180 ELLKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAF 230 E + + T V+ASGGV + +DL + L GV AIVGKA + +F Sbjct: 181 ENTRRINELTRHKVIASGGVRNKEDLDKLGAL---GVRDAIVGKASHNDSF 228 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: 135 Number of extensions: 13 Number of successful extensions: 3 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: 233 Length adjustment: 23 Effective length of query: 217 Effective length of database: 210 Effective search space: 45570 Effective search space used: 45570 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 Jul 26 2024. The underlying query database was built on Jul 25 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