Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate Dsui_1566 Dsui_1566 inositol monophosphatase/fructose-1,6-bisphosphatase family protein
Query= reanno::Korea:Ga0059261_2035 (260 letters) >FitnessBrowser__PS:Dsui_1566 Length = 270 Score = 86.3 bits (212), Expect = 6e-22 Identities = 75/254 (29%), Positives = 110/254 (43%), Gaps = 45/254 (17%) Query: 17 AAGAAIRPYFRAEHGLESKDDSSPVTLADKAAEAAMRRLIIAERPMDAIIGEE------E 70 A A + + +A H KDD + ++ AD A ++ + + + P +IGEE E Sbjct: 23 AREAIVPRFMKAIH--HRKDDGTLLSEADLACQSFLLQRLPEIVPCP-VIGEEMSRAEQE 79 Query: 71 DDRPGTSGRIWVLDPIDGTRSFIVGRPIFGTLIALLEDGWPVLGIIDQPIIKERWLGVTG 130 +G +W +DPIDGT +F+ G P+F IALL + P LGI PI E + G Sbjct: 80 AALEAGNGDVWCIDPIDGTTNFVNGLPVFAVSIALLRERKPRLGITYNPITNELFYAWEG 139 Query: 131 RETLFNGK--PAR---------------ARTCRELSKALLATTSPALFTDGQLHAFEHVD 173 NGK P R R REL A+ T+P F+ Sbjct: 140 GGAYVNGKRLPLRRVAGSLDQAVANVDLKRLPREL--AVRIATAPPFFSQRN-------- 189 Query: 174 AAVMSTVLGGDCYNYGLVASGHLDIVIEAGLKLHDFAALVPVVEGAGGRMCDWQGDPLHA 233 G + VA+G +D+ + G L D+AA +++ AGG MC + D HA Sbjct: 190 -------FGSSALEWCQVAAGRIDVAVHGGQMLWDYAAGCLILKEAGGHMCTLEQDDFHA 242 Query: 234 GS--NGEVIAAGDP 245 ++AA DP Sbjct: 243 DDLWRRRIVAALDP 256 Lambda K H 0.320 0.138 0.419 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: 204 Number of extensions: 10 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: 270 Length adjustment: 25 Effective length of query: 235 Effective length of database: 245 Effective search space: 57575 Effective search space used: 57575 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