Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate GFF1157 PGA1_c11720 inositol-1-monophosphatase SuhB
Query= BRENDA::Q8NS80 (260 letters) >FitnessBrowser__Phaeo:GFF1157 Length = 261 Score = 97.8 bits (242), Expect = 2e-25 Identities = 76/215 (35%), Positives = 107/215 (49%), Gaps = 13/215 (6%) Query: 20 SITLDRFEASDLEVSSKPDMTPVSDADLATEEALREKIATARPADSILGEEFGGDVEFSG 79 S+ D E +L+VS K VS AD+A E+ L+E++ ARP L EE G D Sbjct: 20 SLVKDFREVENLQVSRKGAGDFVSKADIAAEKILKEELMGARPTYGWLAEEGGEDEGVDP 79 Query: 80 -RQWIIDPIDGTKNYVRGVPVWATLIALLDNGKPVAGVISAPALARRWWASEGAGAWRTF 138 R+WI+DP+DGT N++ G+P WA IAL GK VAGV+ A ++A +GAGAW Sbjct: 80 TRRWIVDPLDGTTNFLHGLPHWAISIALEHKGKVVAGVVYDAAKDEMFFAEKGAGAW--- 136 Query: 139 NGSSPRKLSVS----QVSKLDDASLSFSSLSGWAERDLRDQFVSLTDTTWRLRGYG-DFF 193 + ++ VS + + L F+ S L+D L +R +G Sbjct: 137 --MNDTRIRVSGRHRMIESIFATGLPFAGRSD-LPATLQD-LARLMPACAGVRRWGAAAL 192 Query: 194 SYCLVAEGAVDIAAEPEVSLWDLAPLSILVTEAGG 228 VA G + E ++ WDLA I+V EAGG Sbjct: 193 DLAYVAAGRYEGYWERRLNAWDLAAGIIIVQEAGG 227 Lambda K H 0.315 0.133 0.396 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: 182 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 260 Length of database: 261 Length adjustment: 25 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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: 41 (21.6 bits) S2: 47 (22.7 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