Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_009562510.1 RSPH17029_RS00520 inositol monophosphatase family protein
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >NCBI__GCF_000015985.1:WP_009562510.1 Length = 264 Score = 226 bits (576), Expect = 4e-64 Identities = 115/243 (47%), Positives = 155/243 (63%), Gaps = 1/243 (0%) Query: 13 AERLADASGPVIRQYFRTPVAVDDKADASPVTIADREAERTIRAIIEAERPDDGIYGEEF 72 A AD + + ++FR + V+ KAD SPVT+ADR E IR I A PD GI+GEE Sbjct: 11 ANDTADEARRIALKHFRQALDVESKADDSPVTLADRAVEALIRDRIMAAFPDHGIFGEEE 70 Query: 73 GTKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPIVRDRWLGVEG 132 D++ +WV+DPIDGTKS++TG P+FG L+ALL G P LG ID P + +RW G+EG Sbjct: 71 APLRPDSDHLWVVDPIDGTKSYVTGNPLFGGLMALLKDGAPCLGQIDMPALGERWSGIEG 130 Query: 133 RPTLFNGQPARVRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAAKVSVYGGDCYSYG 192 + T FNG+P R +C A A TT P LF GAD + + ++ +GGDCY+Y Sbjct: 131 QATTFNGRPCRTSDCRDP-AEAFAYTTDPMLFTGADAQVLEMLRRSVRMLRFGGDCYAYA 189 Query: 193 LLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLDATSSGRVVAAGDARTHR 252 LLA+G+ DLV+E+GL+ YD+ LV V+ GAGG++TDW G+ L S+G V+AA HR Sbjct: 190 LLASGHCDLVLETGLQPYDYLPLVQVIRGAGGVITDWQGQALGVGSAGEVLAAATPELHR 249 Query: 253 ETL 255 L Sbjct: 250 AML 252 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: 252 Number of extensions: 12 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: 264 Length adjustment: 25 Effective length of query: 235 Effective length of database: 239 Effective search space: 56165 Effective search space used: 56165 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 16 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