Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate N515DRAFT_1749 N515DRAFT_1749 histidinol-phosphatase
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >FitnessBrowser__Dyella79:N515DRAFT_1749 Length = 262 Score = 167 bits (422), Expect = 3e-46 Identities = 106/260 (40%), Positives = 142/260 (54%), Gaps = 12/260 (4%) Query: 1 MTEPCPTPLVTLAERLADASGPVIRQYFRTPVAVDDKADASPVTIADREAERTIRAIIEA 60 M+ P ++ A A+A+ VIR Y+R V V+ K+DA+PVTIADREAE IR +++A Sbjct: 1 MSAPDLQRALSAAREAAEAAAEVIRHYWRRGVEVEIKSDATPVTIADREAELAIRKVLQA 60 Query: 61 ERPDDGIYGEEFGTKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQ 120 P+ IYGEEFG + E +W++DP+DGTKSF+ P F T IAL+H+G VLGV Sbjct: 61 ALPEAAIYGEEFGLDDGARELLWLVDPLDGTKSFVRRTPFFSTQIALMHKGELVLGVSSA 120 Query: 121 PIVRDRWLGVEGRPTLFNGQPARVRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAA- 179 P+ + G F G RV +A A++ T + DA GA Sbjct: 121 PVYGETLWASAGGGAWFEGDRVRV-AATDSMAQASISTGNVKTL---TMDARWAELGAMI 176 Query: 180 ----KVSVYGGDCYSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLD 235 ++ YG C+ Y LLA G DLV+ES + + D AAL +V AGGL TD DG+PL Sbjct: 177 RDSNRIRGYGDFCH-YHLLARGGLDLVIESDVNILDVAALAAIVREAGGLFTDLDGQPL- 234 Query: 236 ATSSGRVVAAGDARTHRETL 255 T R V AG H + L Sbjct: 235 -TLDTRSVLAGTPALHAQAL 253 Lambda K H 0.320 0.139 0.424 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: 211 Number of extensions: 11 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: 262 Length adjustment: 25 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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