Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate Synpcc7942_1763 Synpcc7942_1763 inositol monophosphate family protein
Query= BRENDA::P95189 (260 letters) >FitnessBrowser__SynE:Synpcc7942_1763 Length = 272 Score = 78.2 bits (191), Expect = 2e-19 Identities = 70/238 (29%), Positives = 103/238 (43%), Gaps = 26/238 (10%) Query: 11 ALADRADELTRVRFGALDLRIDTKPDLTPVTDADRAVESDVRQTLGRDRPGDGVLGEEFG 70 AL + + FG L + K D + +T ADR + + L + P +L EE Sbjct: 15 ALCQEVGDRLLLEFGTL--QATEKADGSLITAADRWADQTLCDRLSQLFPKHALLTEE-- 70 Query: 71 GSTTFTGRQW--IVDPIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQRRWWAAR 128 TF G W +VDP+DGT NF +G+P+W +ALL G P G ++ P LQR + Sbjct: 71 SQQTFGGADWTWVVDPLDGTTNFAQGIPIWGISLALLYRGWPVFGAIALPPLQRFYCGVD 130 Query: 129 GRGA-FASVDGA----RPHRLSVSSVAELHSASLSFSS---LSGWARP-GLRERFIGLTD 179 R A V A +P +L S+ SL S L W+ P + R +G + Sbjct: 131 TRSTDLAPVAWAERNHQPLQLRTESLGSNQLFSLCTRSAIVLQRWSAPFPCKIRMLGAST 190 Query: 180 TVWRVRAYGDFLSYCLVAEGAVDIAAEPQVSVWDLAALDIVVREAGGRLTSLDGVAGP 237 ++ V EG A E +WD+AA+ ++ + G SL G P Sbjct: 191 A-----------NFLTVLEGTTLGALEATPKIWDIAAVWVLAQALGADWRSLAGEQFP 237 Lambda K H 0.319 0.136 0.414 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: 179 Number of extensions: 9 Number of successful extensions: 2 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: 260 Length of database: 272 Length adjustment: 25 Effective length of query: 235 Effective length of database: 247 Effective search space: 58045 Effective search space used: 58045 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: 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