Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_013537418.1 THEAM_RS03365 3'(2'),5'-bisphosphate nucleotidase
Query= BRENDA::Q8NS80 (260 letters) >NCBI__GCF_000185805.1:WP_013537418.1 Length = 259 Score = 97.1 bits (240), Expect = 3e-25 Identities = 75/233 (32%), Positives = 118/233 (50%), Gaps = 20/233 (8%) Query: 8 LALALELAELADSITLDRFEASDLEVSSKPDMTPVSDADLATEEALREKIA-TARPADSI 66 L LAL+ + A LD + + EV K D +P+++ADL + + + T P I Sbjct: 5 LNLALKASLDAGKEILDVYGSGSTEVWEKQDRSPLTEADLRSHRVIMNYLRETGYP---I 61 Query: 67 LGEEFGGDVEFSGRQ-----WIIDPIDGTKNYVRGVPVWATLIALLDNGKPVAGVISAPA 121 L EE G D+ + R+ W++DP+DGTK +++ + +AL++NGKP+ GV+ APA Sbjct: 62 LSEE-GKDIPYEERRQWSRFWLVDPLDGTKEFLKRNGEFTVNVALIENGKPILGVVHAPA 120 Query: 122 LARRWWASEGAGAWRTFNGSSPRKLSV-SQVSKLDDASLSFSSLSGWAER---DLRDQFV 177 L ++A G GA++ + SP++L + S V + S S LS ER L+ +F Sbjct: 121 LGVTYFAGVGKGAFKVESEGSPKRLPLFSPVEGVVRVVASRSHLSEETERFVESLKGKFE 180 Query: 178 SLTDTTWRLRGYGDFFSYCLVAEGAVDIAAEPEVSL-WDLAPLSILVTEAGGK 229 + G C+VAEG DI ++ WD A +V AGG+ Sbjct: 181 RV-----EFVAVGSSLKLCMVAEGKADIYPRFAPTMEWDTAAGQAIVEGAGGR 228 Lambda K H 0.315 0.133 0.396 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: 169 Number of extensions: 6 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: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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 (21.6 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