Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate 3606631 Dshi_0063 Inositol-phosphate phosphatase (RefSeq)
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >FitnessBrowser__Dino:3606631 Length = 264 Score = 92.8 bits (229), Expect = 6e-24 Identities = 81/261 (31%), Positives = 118/261 (45%), Gaps = 14/261 (5%) Query: 6 PTPLVTLAERLADASGPVIRQYFRT-PVAVDDKADASPVTIADREAERTIRAIIEAERPD 64 P P + L A A+G + +++R P A D A PVT AD E +R +R + A RPD Sbjct: 2 PAPDLALLIDAAQAAGRIAEKHWRQDPEAWDKAGGAGPVTEADLEVDRMLRTELLAARPD 61 Query: 65 DGIYGEEFGTK--NLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPI 122 G EE LD E V+V+DPIDGT+SF+ G+ F +A++ G PV GV+ P+ Sbjct: 62 YGWLSEETEDTPDRLDRERVFVVDPIDGTRSFMAGQRTFAHALAVVENGIPVAGVVYLPL 121 Query: 123 VRDRWLGVEGRPTLFNGQPARVRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAAKVS 182 + G NG R+ +A AT+ P+L + + A Sbjct: 122 RDKLYTAARGAGAALNGTVLRI-STRSEVAGATVLAARPNL----EGHHWGGTPPALDRH 176 Query: 183 VYGGDCYSYGLLAAGYYD--LVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPL---DAT 237 Y L G +D L + + + +D AA +V AGG TD G L + + Sbjct: 177 FRSSLAYRLALTGEGRFDAMLTLRNSWE-WDIAAGCLIVEEAGGQTTDRHGAGLRFNNPS 235 Query: 238 SSGRVVAAGDARTHRETLAAL 258 + + V A + R H E A L Sbjct: 236 AQTKGVVAANPRLHAELSAKL 256 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: 207 Number of extensions: 10 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 09 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