Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_027721488.1 H589_RS0107710 3'(2'),5'-bisphosphate nucleotidase
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >NCBI__GCF_000425265.1:WP_027721488.1 Length = 251 Score = 70.1 bits (170), Expect = 4e-17 Identities = 71/227 (31%), Positives = 99/227 (43%), Gaps = 16/227 (7%) Query: 16 LADASGPVIRQYFRTPVAVDDKADASPVTIADREAERTIRAIIEAERPDDGIYGEEFGTK 75 +A ++G I + V +KAD SPVT AD + I + PD I EE GTK Sbjct: 11 VARSAGAAIMKVRNKGFEVVNKADKSPVTEADIASNEVISYQLAQMYPDIPILSEE-GTK 69 Query: 76 ---NLDAEWV--WVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPIVRDRWLGV 130 ++W +++DP+DGTK FI F IAL+ + RPVLGV+ P + G Sbjct: 70 ISYTDRSKWTEFFLVDPLDGTKEFIKDNGEFCVCIALMRKNRPVLGVVYAPTQDTLYTGC 129 Query: 131 --EGRPTLFNG---QPARVRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAAKVSVYG 185 G +G Q R R + G +G+ S P D + AK+S Sbjct: 130 AESGAYVSLSGSSPQQIRTRPPSEGEGLIVVGSRS---HPSPDLAEYLDKLNVAKLSP-A 185 Query: 186 GDCYSYGLLAAGYYDLVVESGLKL-YDFAALVPVVTGAGGLMTDWDG 231 G + +A G L + +D AA +V AGG MT DG Sbjct: 186 GSALKFCQVAEGKAHLYPRFNPTMEWDTAAGQAIVEAAGGTMTSLDG 232 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: 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: 251 Length adjustment: 24 Effective length of query: 236 Effective length of database: 227 Effective search space: 53572 Effective search space used: 53572 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