Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate AZOBR_RS09435 AZOBR_RS09435 3'-5'-bisphosphate nucleotidase
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >FitnessBrowser__azobra:AZOBR_RS09435 Length = 257 Score = 79.0 bits (193), Expect = 9e-20 Identities = 75/249 (30%), Positives = 107/249 (42%), Gaps = 26/249 (10%) Query: 1 MTEPCPTPLVTLAERLADASGPVIRQYFRTPVAVDDKADASPVTIADREAERTIRAIIEA 60 MT+ L+ +A +G VI +++ + K D SPVT AD AE I + Sbjct: 1 MTDTAAASLLPKVRTIAHEAGQVILRFYNDGIDAATKVDGSPVTQADLAAEHVITPALHH 60 Query: 61 ERPDDGIYGEEFGTK----NLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLG 116 P + EE ++ W++DP+DGTK FI+ F IAL+ GRPVLG Sbjct: 61 IAPGIPVVAEEAVAAGHRPDISGGRFWLVDPLDGTKEFISRNGEFTVNIALIDGGRPVLG 120 Query: 117 VIDQPIVRDRWLG---------VEGRPTLFNGQPARVRE-CAGGLAAATLGTTSPDLFPG 166 V+ P D + VEGR + P +VR+ GL S G Sbjct: 121 VVYAPATGDLYAACGAGTAVHWVEGR----HDYPIQVRKPPPDGLTV----VASRSHGSG 172 Query: 167 ADQDAFRRVAG-AAKVSVYGGDCYSYGLLAAGYYDLVVESG-LKLYDFAALVPVVTGAGG 224 ++ D F +AG K V G + +A+G DL G +D AA ++ AGG Sbjct: 173 SELDGF--LAGYTVKNRVTCGSSLKFCTVASGKADLYPRFGPTSEWDTAAGHAILAAAGG 230 Query: 225 LMTDWDGRP 233 + DG P Sbjct: 231 RVEQPDGSP 239 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: 234 Number of extensions: 9 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: 257 Length adjustment: 24 Effective length of query: 236 Effective length of database: 233 Effective search space: 54988 Effective search space used: 54988 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