Align phosphoribosylanthranilate isomerase; EC 5.3.1.24 (characterized)
to candidate Pf1N1B4_6 Phosphoribosylanthranilate isomerase (EC 5.3.1.24)
Query= CharProtDB::CH_008324 (213 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6 Length = 145 Score = 118 bits (295), Expect = 6e-32 Identities = 67/147 (45%), Positives = 91/147 (61%), Gaps = 11/147 (7%) Query: 4 RAKICGITRSQDVQAAVSAGADAIGLVFFPPSPRHVSIAQAQALLQHIPAYVQVVGLFVN 63 R+KICGITR +D AAV AGADAIG VF+ SPR V++ QA+A+++ +P +V VGLFVN Sbjct: 5 RSKICGITRIEDALAAVEAGADAIGFVFYAKSPRAVTVQQARAIIKALPPFVTTVGLFVN 64 Query: 64 ATADQIKSVLDCVALDVLQLHGDETPEQCQEIALQCKRRWYKAIQVKPELDVVDEVQRYQ 123 A+ ++ +LD V LD+LQ HGDET C+ R + KA++VK D+ Y Sbjct: 65 ASRCELGEILDAVPLDLLQFHGDETAADCE----GWHRPYIKALRVKAGDDIAAACDAY- 119 Query: 124 AAGASAVLLDAW-----HPELKGGTGH 145 A AS +LLD + +K TGH Sbjct: 120 -ASASGILLDTYVEGVPGEPVKRSTGH 145 Lambda K H 0.321 0.135 0.404 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: 83 Number of extensions: 3 Number of successful extensions: 1 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: 213 Length of database: 145 Length adjustment: 19 Effective length of query: 194 Effective length of database: 126 Effective search space: 24444 Effective search space used: 24444 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 44 (21.6 bits)
Align phosphoribosylanthranilate isomerase; EC 5.3.1.24 (characterized)
to candidate Pf1N1B4_5 Phosphoribosylanthranilate isomerase (EC 5.3.1.24)
Query= CharProtDB::CH_008324 (213 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5 Length = 46 Score = 52.8 bits (125), Expect = 1e-12 Identities = 25/43 (58%), Positives = 32/43 (74%) Query: 165 LTPENVVDAIQTTHAFAVDVSGGVEAAKGIKDKQLIERFMQGV 207 LTP+NV +AI +AVDVSGGVEA+KGIKD I+ F++ V Sbjct: 1 LTPDNVAEAIARVRPYAVDVSGGVEASKGIKDHARIQAFIKAV 43 Lambda K H 0.321 0.135 0.404 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: 31 Number of extensions: 1 Number of successful extensions: 1 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: 213 Length of database: 46 Length adjustment: 10 Effective length of query: 203 Effective length of database: 36 Effective search space: 7308 Effective search space used: 7308 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (20.9 bits) S2: 39 (19.6 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