Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate Pf1N1B4_869 Inositol-1-monophosphatase (EC 3.1.3.25)
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_869 Length = 272 Score = 99.0 bits (245), Expect = 9e-26 Identities = 85/263 (32%), Positives = 123/263 (46%), Gaps = 15/263 (5%) Query: 8 PLVTLAERLA-DASGPVIRQYFRTP-VAVDDKADASPVTIADREAERTIRAIIEAERPDD 65 P++ +A R A AS + R R + VD+K V+ DR AE+ I + P+ Sbjct: 3 PMLNIALRAARSASELIFRSIERLDTIKVDEKDAKDYVSEVDRAAEQKIIDALRKAYPNH 62 Query: 66 GIYGEEFGTKNLDA----EWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQP 121 I GEE G E++W+IDP+DGT +F+ G P F IA +RGR V+ P Sbjct: 63 SIMGEETGMHAGSGIEGEEYLWIIDPLDGTTNFLRGIPHFAVSIACKYRGRLEHAVVLDP 122 Query: 122 IVRDRWLGVEGRPTLFNGQPARVRECAGGLAAATLGTTSP---DLFPGADQ--DAFRRVA 176 + ++ + GR NG+ RV L A LGT P D D FR + Sbjct: 123 VRQEEFTASRGRGAQLNGRRLRV-SGRTSLDGALLGTGFPFRDDQMDNLDNYLGMFRALV 181 Query: 177 G-AAKVSVYGGDCYSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLD 235 G A + G +AAG +D ESGL +D AA ++ AGGL++D+ G D Sbjct: 182 GQTAGIRRAGSASLDLAYVAAGRFDAFWESGLSEWDMAAGALLIQEAGGLVSDFTGGH-D 240 Query: 236 ATSSGRVVAAGDARTHRETLAAL 258 G +V AG+ + + L A+ Sbjct: 241 FLEKGHIV-AGNTKCFKAVLTAI 262 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: 154 Number of extensions: 7 Number of successful extensions: 3 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: 272 Length adjustment: 25 Effective length of query: 235 Effective length of database: 247 Effective search space: 58045 Effective search space used: 58045 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