Align Probable histidinol-phosphatase; HolPase; EC 3.1.3.15 (uncharacterized)
to candidate WP_051327199.1 G491_RS30500 PHP domain-containing protein
Query= curated2:Q9RX45 (260 letters) >NCBI__GCF_000429905.1:WP_051327199.1 Length = 266 Score = 154 bits (390), Expect = 1e-42 Identities = 87/256 (33%), Positives = 140/256 (54%), Gaps = 4/256 (1%) Query: 4 LCDSHLHTPLCGHATGTPREYAQAALDAGLSGLCFTDHMPMPRWYDAPWRMKLEQLPEYI 63 L D H+HTPLC HA G Y Q A+ GL+ +CF DH+ + R + M +++P Y Sbjct: 3 LIDYHVHTPLCNHAKGEMEAYVQQAVKLGLAEICFLDHLTL-RPDGSFLSMSPQEVPLYH 61 Query: 64 AEIQAVQQEFAGRLDVRLGLEADFHPGTEKFVEKVLGMFDWDYVIGSVHYLGAWGFDNPE 123 ++ + ++ R+ V++GLE DF T + +++ +D + GSVH++G W + + Sbjct: 62 RAVKRLAAKYEDRIWVKVGLEVDFDLETMEQAMEIVDAHSFDAIGGSVHFIGEWNMVSHK 121 Query: 124 FVAEYEERDLGGLYRDYYALVEGAARSGLFDAIGHLDLPKKFGHLDPDPVYAL--HALDV 181 R+ ++ +Y +E A FD + HLD+ KFG D + +DV Sbjct: 122 ERDNCPFRECEDMFAEYLNHLETMAEHSFFDFLCHLDVVGKFGDSPQDRMENRWDQVIDV 181 Query: 182 VAGQGLALDFNTAGWRKPVAEAYPAPDLVRAAAERGIPFVLGSDAHQPGEVGFRFADAVK 241 +AG+GLA++ NT+G R P E YP+ +++ + G+P LGSDAH P +VG F +AV Sbjct: 182 IAGKGLAVEINTSGKRHPKGELYPSLWILQKLNQAGVPITLGSDAHSPKQVGMDFDEAVS 241 Query: 242 EIRDVGGRTV-TFRHR 256 R+ G ++ TF HR Sbjct: 242 LAREAGYHSLATFSHR 257 Lambda K H 0.322 0.142 0.455 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: 226 Number of extensions: 11 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: 266 Length adjustment: 25 Effective length of query: 235 Effective length of database: 241 Effective search space: 56635 Effective search space used: 56635 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 (21.9 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