Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_012042778.1 BBTA_RS12125 histidinol phosphate phosphatase
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >NCBI__GCF_000015165.1:WP_012042778.1 Length = 262 Score = 237 bits (605), Expect = 2e-67 Identities = 127/251 (50%), Positives = 160/251 (63%), Gaps = 3/251 (1%) Query: 10 VTLAERLADASGPVIRQYFRTPVAVDDKADASPVTIADREAERTIRAIIEAERPDDGIYG 69 + A LAD P+ YFRT V K+D SPVT+ADR E +R I A P GIYG Sbjct: 15 LAFAAELADEVRPIALSYFRTAVEFTAKSDDSPVTVADRLIEARLRERISARYPSHGIYG 74 Query: 70 EEFGTKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPIVRDRWLG 129 EE G K DA + WVIDPIDGTKSFITG P+FGTLI L +P G+ID P +RW+G Sbjct: 75 EEMGVKQGDA-FTWVIDPIDGTKSFITGFPLFGTLIGLTCDRQPFCGLIDIPATGERWIG 133 Query: 130 VEGRPTLFNGQPARVRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAAKVSVYGGDCY 189 G T + G +R R+C +A A TTSPD F AD+ F R++ AAK+ +GGDCY Sbjct: 134 RPGLTT-YGGVRSRTRDCRR-VADARFYTTSPDTFADADRARFERLSNAAKMRRFGGDCY 191 Query: 190 SYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLDATSSGRVVAAGDAR 249 YGLLA+G+ DL++E+GL+ YD+ ALVP++ AGG +TDWDG PL SSG V+A+ Sbjct: 192 IYGLLASGHCDLILETGLQPYDYMALVPILEAAGGRITDWDGAPLSVESSGHVLASATPA 251 Query: 250 THRETLAALAG 260 H E LA + G Sbjct: 252 LHDEALAIIRG 262 Lambda K H 0.320 0.139 0.424 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: 261 Number of extensions: 11 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: 262 Length adjustment: 25 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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 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