Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_043878940.1 AZC_RS05545 3'(2'),5'-bisphosphate nucleotidase CysQ
Query= reanno::Korea:Ga0059261_2035 (260 letters) >NCBI__GCF_000010525.1:WP_043878940.1 Length = 266 Score = 65.9 bits (159), Expect = 8e-16 Identities = 72/234 (30%), Positives = 95/234 (40%), Gaps = 13/234 (5%) Query: 13 RLADAAGAAIRPYFRAEHGLESKDDSSPVTLADKAAEAAMRRLIIAERPMDAIIGEEEDD 72 R+A AGA IR K D+S VT AD+AAEA + + P II EE Sbjct: 15 RIALDAGAVIRRIEANGIHAREKADASVVTDADEAAEALICPALRTLAPGTPIIAEEAVA 74 Query: 73 RPG---TSGRIWVLDPIDGTRSFIVGRPIFGTLIALLEDGWPVLGIIDQPIIKERWLGVT 129 G R +++DP+DGTR F+ G + IAL+EDG P GII P + G Sbjct: 75 AGGGVAPGRRFFLVDPLDGTREFVSGNGEYTVNIALVEDGTPRYGIIYAPAKGLLYAGGD 134 Query: 130 GRETLFNGKPARART--------CRELSKALLATTSPALFTDGQLHAFEHVDAAVMSTVL 181 G P A CR + + +D AF V V Sbjct: 135 GAAFKALRAPEDAVVPESWTPIHCRLRPAGPIRVCASRSHSDPSTSAFIG-GFEVEDCVN 193 Query: 182 GGDCYNYGLVASGHLDIVIEAGLKLH-DFAALVPVVEGAGGRMCDWQGDPLHAG 234 G +GL+A G +D+ + D AA +V AGG + G PL G Sbjct: 194 AGSALKFGLLAEGAVDLYPRLSPVMEWDSAAGHAIVVAAGGSVRRPDGSPLTYG 247 Lambda K H 0.320 0.138 0.419 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: 237 Number of extensions: 19 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: 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 (21.8 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