Align Histidinol-phosphatase; Hol-Pase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate N515DRAFT_2110 N515DRAFT_2110 phosphatidylglycerophosphatase C
Query= SwissProt::Q9I6F6 (217 letters) >FitnessBrowser__Dyella79:N515DRAFT_2110 Length = 225 Score = 50.1 bits (118), Expect = 3e-11 Identities = 45/151 (29%), Positives = 71/151 (47%), Gaps = 24/151 (15%) Query: 58 QAFTQAILGRTEMAQLETWHRQFMQEVIEPIVLAKGEALLAEHRAAGDRLVIITATNRFV 117 QAF A++ R RQF ++ G +L H+AAGDR++++T R V Sbjct: 87 QAFAAALVRRP---------RQFYRD---------GLQVLRRHQAAGDRVIVVTGCERTV 128 Query: 118 TGPIAERLGVETLIATECEMRDGRYTGQTFDVPCFQGGKVVRLQRWLDENGLDLEGASFY 177 I ++LG+E L E + G + + F +L+R L +G+ E Y Sbjct: 129 ARGILDQLGLEGLELLASEFKPGPFGMRV----KFHNVGRRKLER-LAAHGVK-EWQLAY 182 Query: 178 SDSLNDLPLLEKVSRPVAVDPDPRLRAEAEK 208 SDSL D+P+L+ V V+ P++ EK Sbjct: 183 SDSLADIPMLKGAGEAVLVNGTPKVCKRLEK 213 Lambda K H 0.321 0.138 0.418 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: 141 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 217 Length of database: 225 Length adjustment: 22 Effective length of query: 195 Effective length of database: 203 Effective search space: 39585 Effective search space used: 39585 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 (21.9 bits) S2: 45 (21.9 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