Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate GFF3890 Psest_3960 3'(2'),5'-bisphosphate nucleotidase, bacterial
Query= BRENDA::P95189 (260 letters) >FitnessBrowser__psRCH2:GFF3890 Length = 272 Score = 80.5 bits (197), Expect = 3e-20 Identities = 75/221 (33%), Positives = 100/221 (45%), Gaps = 24/221 (10%) Query: 28 DLRIDTKPDLTPVTDADRAVESDVRQTLGRDRPGDGVLGEE-----FGGSTTFTGRQWIV 82 +L + K D +PVT AD A + L VL EE ++T R W+V Sbjct: 27 ELAVQAKADDSPVTAADMAAHRVLADGLRALDGAIPVLSEEDCELSLAERASWT-RWWLV 85 Query: 83 DPIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQRRWWAARGRGAFAS-VDGA-- 139 DP+DGTK F+ G + +AL+E+G GVV PA R ++ GA+ S DGA Sbjct: 86 DPLDGTKEFIAGSEEFTVNVALIEEGKVRFGVVGIPASGRCYYGGEDFGAWRSEADGAAE 145 Query: 140 --RPHRLSVSS---VAELHSASLSFSSLSGWARPGLRERFIGLTDTVWRVRAYGDFLSYC 194 R R V + VA +S + L G L ERF L + G L +C Sbjct: 146 PLRVRRQPVDAFTVVASRRHSSPAQEQLLG----RLGERFGELA-----LANVGSSLKFC 196 Query: 195 LVAEGAVDIAAE-PQVSVWDLAALDIVVREAGGRLTSLDGV 234 L+AEGA D S WD AA V+ AGG + + GV Sbjct: 197 LLAEGAADCYPRLAPTSQWDTAAAQGVLEGAGGEVLDVSGV 237 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: 197 Number of extensions: 7 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: 272 Length adjustment: 25 Effective length of query: 235 Effective length of database: 247 Effective search space: 58045 Effective search space used: 58045 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