Align Histidinol-phosphatase; HolPase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate GFF2461 HP15_2405 3'(2'), 5'-bisphosphate nucleotidase
Query= SwissProt::P95189 (260 letters) >FitnessBrowser__Marino:GFF2461 Length = 258 Score = 96.3 bits (238), Expect = 6e-25 Identities = 76/233 (32%), Positives = 110/233 (47%), Gaps = 20/233 (8%) Query: 10 LALADRADELTRVRFGALDLRIDTKPDLTPVTDADRAVESDVR---QTLGRDRPGDGVLG 66 + +AD A E + D ++ K D +P+T AD A + +++ RD P +L Sbjct: 11 IKVADAASEKV-LHIYQSDFKVSYKADASPITAADTAAHDIITHGLRSISRDIP---ILS 66 Query: 67 EEFGGSTTFTGRQ-----WIVDPIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQ 121 EE G + R+ W+VDP+DGTK+F + + IA++EDG P +GVV APAL+ Sbjct: 67 EE-GSDIPWEERKHWRRFWLVDPVDGTKDFTQRTGEFTVNIAMIEDGQPVMGVVIAPALK 125 Query: 122 RRWWAARGRGAFASVDGARPHRLSVSSVAELHSASLSFSSLSGWARPGLRERFIGLTDTV 181 +W G GA R H + V+ L S + L+ R FI Sbjct: 126 EAFWGIVGEGAHMRDRTGRVHHIRVAEPKPLKRVVASKNHLNEETR-----AFIEALGDH 180 Query: 182 WRVRAYGDFLSYCLVAEGAVDIAAE-PQVSVWDLAALDIVVREAGGRLTSLDG 233 V+A G L C +AEG DI S WD A V+ AGG++ +LDG Sbjct: 181 ELVQA-GSSLKLCRIAEGHADIYPRLGPTSEWDTGAAQAVLMAAGGKVQTLDG 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: 136 Number of extensions: 5 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: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 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