Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_081433973.1 AZC_RS12315 3'(2'),5'-bisphosphate nucleotidase CysQ
Query= BRENDA::Q8NS80 (260 letters) >NCBI__GCF_000010525.1:WP_081433973.1 Length = 279 Score = 103 bits (258), Expect = 3e-27 Identities = 87/261 (33%), Positives = 123/261 (47%), Gaps = 31/261 (11%) Query: 10 LALELAELADSITLDRFEASDLEVSSKPDMTPVSDADLATEEALREKIATARPADSILGE 69 L + A +I LD F A LE SK + +PV+ AD+A + L+++ P L E Sbjct: 25 LMADAVTAAGAIALDMFRAGRLESWSKANDSPVTAADIAVDRFLKDRFTALAPDYGWLSE 84 Query: 70 EF--GGDVEFSGRQWIIDPIDGTKNYVRGVPVWATLIALLDNGKPVAGVISAPALARRWW 127 E D R W++DPIDGT+ ++ G WA AL++NG+PVA + APA + Sbjct: 85 ESVDSPDRLARSRVWVVDPIDGTRGFMAGGVDWAVSAALVENGRPVAAALFAPASEELFV 144 Query: 128 ASEGAGAWRTFNGSSPRKLSVSQVSKLDDASLS--FSSLSGWAERDLRDQFVSLTDTTWR 185 AS GAGA R NG L+VS ++ L A +S +SL A+ ++ + R Sbjct: 145 ASVGAGATR--NGV---PLAVSDLTALAGARISGPVASLDRLAQHAPIERRPRVRSLALR 199 Query: 186 LRGYGDFFSYCLVAEGAVDIA-AEPEVSLWDLAPLSILVTEAGGKFTSLAGVDG------ 238 + VA +D+A A P WD+A +LV EAGG L+G+DG Sbjct: 200 I---------TRVATAELDVALAAPNAHDWDIAAADLLVQEAGG---LLSGLDGRPLTYN 247 Query: 239 ---PHGGDAVATNGILHDETL 256 P G V LH L Sbjct: 248 ATVPRHGALVCAGTALHPHIL 268 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: 230 Number of extensions: 13 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: 279 Length adjustment: 25 Effective length of query: 235 Effective length of database: 254 Effective search space: 59690 Effective search space used: 59690 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 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