Align phosphoribosylanthranilate isomerase subunit (EC 5.3.1.24) (characterized)
to candidate WP_012282979.1 HM1_RS08635 phosphoribosylanthranilate isomerase
Query= metacyc::MONOMER-301 (205 letters) >NCBI__GCF_000019165.1:WP_012282979.1 Length = 226 Score = 140 bits (354), Expect = 1e-38 Identities = 97/214 (45%), Positives = 122/214 (57%), Gaps = 21/214 (9%) Query: 3 RVKICGITNLEDALFSVESGADAVGFVFYPKSKRYISPEDARRISVELPPFVFRVGVFVN 62 RVKICGI + +DA ++ +GA A+ F F S+RYI PE AR I +ELPPFV VGVF + Sbjct: 6 RVKICGIRSFQDAEAALGAGAHAIAFNFVRPSRRYIHPEAAREIILELPPFVSVVGVFAD 65 Query: 63 EEPEKILDVASYVQLNAVQLHGEEPIELCRKIAERILVIKA-----------VGVSNERD 111 E + ++AS+ +L A+Q HGEE E CR+ + VIKA G + D Sbjct: 66 EPRYSVEEIASFCRLQALQFHGEETPEYCRRWS--YPVIKAFRFGDGAPAAKAGATAFTD 123 Query: 112 ME----RALNYREFPILLDTKTPE-YGGSGKTFDWSLILPYRDRFRYLVLSGGLNPENVR 166 E A Y L+D P GG G+ FDWS I R R R L+L+GGLNP NVR Sbjct: 124 WESLAQAAHEYDVNAFLIDAYCPNALGGMGRAFDWSKI-GGRLR-RPLILAGGLNPNNVR 181 Query: 167 SAIDVVRPFAVDVSSGVEAFPGKKDHDSIKMFIK 200 AI VRPF VDV+SGVE GKKD F++ Sbjct: 182 EAIVRVRPFGVDVASGVET-DGKKDLAKAAAFVE 214 Lambda K H 0.321 0.140 0.408 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: 144 Number of extensions: 6 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: 205 Length of database: 226 Length adjustment: 22 Effective length of query: 183 Effective length of database: 204 Effective search space: 37332 Effective search space used: 37332 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: 45 (21.9 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