Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_069661634.1 BCR25_RS00405 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::P16250 (240 letters) >NCBI__GCF_001730305.1:WP_069661634.1 Length = 251 Score = 86.7 bits (213), Expect = 4e-22 Identities = 64/210 (30%), Positives = 108/210 (51%), Gaps = 15/210 (7%) Query: 6 LLPAVDVRDGQAVRLVHGESGTETSYGSPLEAALAWQRSGAEWLHLVDLDAAFGTGDNRA 65 ++P +DV DG+ V+ V+ + + G P++ A A+ GA+ L +D+ A T D R Sbjct: 6 IIPCLDVTDGRVVKGVNFVNLQDV--GDPVDIARAYNEQGADELVFLDITA---TSDERQ 60 Query: 66 LIAEV----AQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEH 121 + +V A + I + + GGIR D + L G +++L +AA++ PE + + Sbjct: 61 TMVDVVTRTAAEVFIPLTVGGGIRCIDDMRKLLQAGADKISLNSAAIKQPELIQAGAEKF 120 Query: 122 GDK-IAVGLDVRGTT----LRGRGWTRDGG-DLYETLDRLNKEGCARYVVTDIAKDGTLQ 175 G + + V +D + + + +G D G D E + G ++T + DGT Sbjct: 121 GSQCMVVAIDAKRSGDSWHVFVKGGREDTGLDAIEWAKKAVSLGAGEILLTSMDADGTKN 180 Query: 176 GPNLELLKNVCAATDRPVVASGGVSSLDDL 205 G +LEL + VCAA + PV+ASGG S DD+ Sbjct: 181 GYDLELNQAVCAAVNVPVIASGGCGSADDI 210 Score = 30.0 bits (66), Expect = 4e-05 Identities = 15/66 (22%), Positives = 29/66 (43%) Query: 143 RDGGDLYETLDRLNKEGCARYVVTDIAKDGTLQGPNLELLKNVCAATDRPVVASGGVSSL 202 +D GD + N++G V DI + ++++ A P+ GG+ + Sbjct: 27 QDVGDPVDIARAYNEQGADELVFLDITATSDERQTMVDVVTRTAAEVFIPLTVGGGIRCI 86 Query: 203 DDLRAI 208 DD+R + Sbjct: 87 DDMRKL 92 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: 151 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 240 Length of database: 251 Length adjustment: 24 Effective length of query: 216 Effective length of database: 227 Effective search space: 49032 Effective search space used: 49032 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