Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_066917818.1 ACG33_RS00190 3'(2'),5'-bisphosphate nucleotidase
Query= reanno::Phaeo:GFF2154 (250 letters) >NCBI__GCF_001579945.1:WP_066917818.1 Length = 270 Score = 73.9 bits (180), Expect = 3e-18 Identities = 73/236 (30%), Positives = 105/236 (44%), Gaps = 21/236 (8%) Query: 1 MADAARQA---ILPYFRSAGLQSDNKLDEGFDPVTIADRAAEQAMRSVLSELRPEDSILG 57 + D AR+A IL + S + K D+ PVT+AD A + L L PE +L Sbjct: 13 IVDIARRAGEEILEVYASQDAGARTKADDS--PVTLADLRAHSVIEGALQALTPEIPLLS 70 Query: 58 EEFG-----ETHGQSGRTWVLDPIDGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIG 112 EE E + R W++DP+DGTR F++ + V IAL +A P LG+V P Sbjct: 71 EESAQLLPYEQRARWSRYWLVDPLDGTREFLARNGEFTVNIALIEAHAPTLGVVHVPVRK 130 Query: 113 ERFIGTPEGASLTGPLGHSALVTRATDSLSEATLFTTFPEVGTEAER-AAFQRVSAQV-- 169 + G P G G +A A +A + VG+++ R + + AQ+ Sbjct: 131 TTYAGLP-GVGAWRRHGTAA----AEPIHVQARAASPVRVVGSKSHRGTSLDGLLAQLGP 185 Query: 170 -RLTRYGMDCYAYALLAAGQCDLVIEAG-LNAYDIQAPIAVIQAAGGVVTNWQGEP 223 L G + L+A G DL G + +D A AV+ AAGG V G P Sbjct: 186 HELLSVG-SSLKFCLIAEGTADLYPRLGPTSEWDTAAAQAVVCAAGGAVVKLDGTP 240 Lambda K H 0.317 0.134 0.392 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: 165 Number of extensions: 8 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: 250 Length of database: 270 Length adjustment: 24 Effective length of query: 226 Effective length of database: 246 Effective search space: 55596 Effective search space used: 55596 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 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