Align Histidinol-phosphatase; HolPase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate 7022920 Shewana3_0170 3'(2'),5'-bisphosphate nucleotidase (RefSeq)
Query= SwissProt::P95189 (260 letters) >FitnessBrowser__ANA3:7022920 Length = 270 Score = 82.0 bits (201), Expect = 1e-20 Identities = 69/224 (30%), Positives = 96/224 (42%), Gaps = 7/224 (3%) Query: 10 LALADRADELTRVRFGALDLRIDTKPDLTPVTDADRAVESDVRQTLGRDRPGDGVLGEEF 69 +A+A A R + + +TK D TPVT AD A + + L P +L EE Sbjct: 11 IAIATDAGRTIREIYLKGNFERETKSDNTPVTSADLAANQLICERLAALTPDIPILSEEA 70 Query: 70 GGSTTFTG----RQWIVDPIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQRRWW 125 R W+VDP+DGT F+ G ++ +IAL+E P +GVV P Q ++ Sbjct: 71 ADIPLSVREGWKRYWLVDPLDGTGEFIAGSGDFSVIIALVEHNRPVMGVVYVPMTQVCYY 130 Query: 126 AARGRGAFASVDGARPHRLSVSSVAELHSASLSFSSLSGWARPGLRERFIGLTDTVWRVR 185 A G GA+ D + R+S + SL ++S P V Sbjct: 131 AIAGLGAYKRTD-KQEVRISSRQIQHREQVSLRL-AVSRRQDPQSVLTLFNQPKHCELVV 188 Query: 186 AYGDFLSYCLVAEGAVDIAAE-PQVSVWDLAALDIVVREAGGRL 228 G L CLVAEG D WD A I++ EAGG+L Sbjct: 189 MGGAALKSCLVAEGRADCYVRVGPTGEWDTGAAQIIIEEAGGQL 232 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: 127 Number of extensions: 6 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: 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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