Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_093427373.1 BM272_RS03710 3'(2'),5'-bisphosphate nucleotidase CysQ
Query= BRENDA::P95189 (260 letters) >NCBI__GCF_900112605.1:WP_093427373.1 Length = 269 Score = 94.7 bits (234), Expect = 2e-24 Identities = 78/228 (34%), Positives = 108/228 (47%), Gaps = 12/228 (5%) Query: 11 ALADRADELTRVRFGALDLRIDTKPDLTPVTDADRAVESDVRQTLGRDRPGDGVLGEEFG 70 A+A RA E + D ++TK D +P+T+ADRA + + L P VL EE G Sbjct: 10 AIAHRAGEAILDVYHRADQGVETKADDSPLTEADRAAHRIIAEALAEAYPDIPVLSEE-G 68 Query: 71 GSTTFT-----GRQWIVDPIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQRRWW 125 + R ++VDP+DGTK F+ + IAL+E+G P GVV APAL R + Sbjct: 69 AEIPYAERAHWSRLFVVDPLDGTKEFLHKNGEFTVNIALVEEGEPVAGVVHAPALGRT-Y 127 Query: 126 AARGRGAFASVDGARPHRLSVSSVAELHSASLSFSSLSGWARPGLRERFIGLTDTVWRVR 185 G GA + DGARP +++ + A P ++ L + + Sbjct: 128 LGDGNGA-SRRDGARP-PMAIRVADPVAGRPWRVVGSRSHATPEVQALVDALGEA--ELV 183 Query: 186 AYGDFLSYCLVAEGAVDIAAE-PQVSVWDLAALDIVVREAGGRLTSLD 232 + G L CLVAEGA D+ S WD AA VVR AGG + D Sbjct: 184 SMGSSLKLCLVAEGAADLYPRLGPTSEWDTAAAHAVVRAAGGVVVDTD 231 Lambda K H 0.319 0.136 0.414 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: 162 Number of extensions: 10 Number of successful extensions: 4 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: 269 Length adjustment: 25 Effective length of query: 235 Effective length of database: 244 Effective search space: 57340 Effective search space used: 57340 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 Jul 25 2024. The underlying query database was built on Jul 25 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