Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_057508177.1 ABB28_RS08265 3'(2'),5'-bisphosphate nucleotidase CysQ
Query= BRENDA::P95189 (260 letters) >NCBI__GCF_001431535.1:WP_057508177.1 Length = 275 Score = 82.4 bits (202), Expect = 9e-21 Identities = 73/231 (31%), Positives = 106/231 (45%), Gaps = 14/231 (6%) Query: 5 DLMLALALADRADELTRVRFGALDLRIDTKPDLTPVTDADRAVESDVRQTLGRDRPGDGV 64 + ++A+A D A + +V D+ + K D +PVT AD A + L R P + Sbjct: 12 ETVIAIA-QDAAAAIMQVYASGFDITL--KADDSPVTAADLAAHQRIVSGLSRLTPDLPI 68 Query: 65 LGEEFGGSTTFT----GRQWIVDPIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPAL 120 L EE + T G W+VDP+DGT+ F++ ++ IAL+ G P+ GVV AP Sbjct: 69 LSEEATAAAWETRRHWGAYWLVDPLDGTREFIKRNGEFSVNIALVYQGAPTFGVVLAPVT 128 Query: 121 QRRWWAARGRGAFASVDGARPHRLSVSSVAELHSASLSFSSLSGWARPGLRERFIGLTDT 180 W A RG A+ GA L A+ + S L +R +G +T Sbjct: 129 GLVWHAMRGEQAYRR-QGAHDTVLRTRVPAQSPLRVAASRSHRSARTQALLDR-MGDIET 186 Query: 181 VWRVRAYGDFLSYCLVAEGAVDIAAE-PQVSVWDLAALDIVVREAGGRLTS 230 V A G L +C +AEG +D+ S WD AA V+ AGG + S Sbjct: 187 V----AQGSSLKFCRIAEGDLDVYPRLGPTSEWDTAAGQCVLHAAGGAVLS 233 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: 159 Number of extensions: 6 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: 275 Length adjustment: 25 Effective length of query: 235 Effective length of database: 250 Effective search space: 58750 Effective search space used: 58750 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