Align phosphoribosylanthranilate isomerase subunit (EC 5.3.1.24) (characterized)
to candidate WP_013553121.1 NITSA_RS00800 phosphoribosylanthranilate isomerase
Query= metacyc::MONOMER-301 (205 letters) >NCBI__GCF_000186245.1:WP_013553121.1 Length = 196 Score = 134 bits (337), Expect = 1e-36 Identities = 88/207 (42%), Positives = 119/207 (57%), Gaps = 14/207 (6%) Query: 2 VRVKICGITNLEDALFSVESGADAVGFVFYPKSKRYISPEDARRISVELPPFVFRVGVFV 61 ++VKICGITN DA+ S+E+GADA+GFVFYPKS RYI+PE AR I LPPFV +VG+FV Sbjct: 1 MKVKICGITNYNDAMRSIEAGADALGFVFYPKSPRYITPEAAREIIDRLPPFVEKVGLFV 60 Query: 62 NEEPEKILDVASYVQLNAVQLHGEEPIELCRKIAERILVIKAVGVSNERDME-RALNYRE 120 PE+I +A + Q+H + ++ A V+ V D+E A YR Sbjct: 61 ENTPEEIERMAKMGGITLAQIHFD--VDEAFLDAVDFPVLPVVRARRLEDLECFADRYR- 117 Query: 121 FPILLDTKTPEYGGSGK--TFDWSLILPYRDRFRYLVLSGGLNPENVRSAIDVVRPFAVD 178 L+D YGGSGK +W RD R ++++GGL P+NV + + D Sbjct: 118 ---LVDAYCEAYGGSGKRLNLEW---FEGRDNSR-IIIAGGLTPDNVEE-LRGYGFYGCD 169 Query: 179 VSSGVEAFPGKKDHDSIKMFIKNAKGL 205 VSSG EA G+KD + + FI+ AK L Sbjct: 170 VSSGTEAAKGRKDPEKVMRFIERAKSL 196 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: 150 Number of extensions: 11 Number of successful extensions: 4 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: 196 Length adjustment: 21 Effective length of query: 184 Effective length of database: 175 Effective search space: 32200 Effective search space used: 32200 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