Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate Ac3H11_3645 Inositol-1-monophosphatase (EC 3.1.3.25)
Query= BRENDA::Q8NS80 (260 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3645 Length = 318 Score = 91.7 bits (226), Expect = 2e-23 Identities = 74/235 (31%), Positives = 115/235 (48%), Gaps = 13/235 (5%) Query: 8 LALALELAELADSITLDR--FEASDLEVSSKPDMTPVSDADLATEEALREKIATARPADS 65 L +A++ A A +I ++R + + +S K V++ D A+E+ + E + TA P Sbjct: 9 LNVAIKAARAAGAI-INRAALDVESVRISQKQINDFVTEVDHASEKIIIETLLTAYPGHG 67 Query: 66 ILGEEFGGDVEFSGRQ--WIIDPIDGTKNYVRGVPVWATLIALLDNGKPVAGVISAPALA 123 IL EE G + + WIIDP+DGT N++ G PV+ IAL GK V+ P Sbjct: 68 ILAEESGKEYGAKDSEFVWIIDPLDGTTNFIHGFPVYCISIALAVKGKVEQAVVYDPTRN 127 Query: 124 RRWWASEGAGAWRTFNGSSPRKLSVSQVSKLDDASLS--FSSLSGWAERDLRDQFVSLTD 181 + A++G GA+ + R++ VS+ ++L D +S F G + + + Sbjct: 128 DLFTATKGRGAY-----LNERRIRVSKRTQLKDCLISTGFPFRPGDNFKSYLNMMADVMQ 182 Query: 182 TTWRLRGYG-DFFSYCLVAEGAVDIAAEPEVSLWDLAPLSILVTEAGGKFTSLAG 235 T LR G VA G D E +S+WD+A S+LVTEAGG + G Sbjct: 183 RTAGLRRPGAAALDLAYVAAGFTDGFFETGLSIWDVAAGSLLVTEAGGLVGNFTG 237 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: 180 Number of extensions: 8 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: 318 Length adjustment: 26 Effective length of query: 234 Effective length of database: 292 Effective search space: 68328 Effective search space used: 68328 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