Align Histidinol-phosphatase; HolPase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate WP_017596874.1 D471_RS0100845 histidinol-phosphatase
Query= SwissProt::Q9K4B1 (266 letters) >NCBI__GCF_000341125.1:WP_017596874.1 Length = 266 Score = 338 bits (868), Expect = 5e-98 Identities = 173/263 (65%), Positives = 198/263 (75%), Gaps = 4/263 (1%) Query: 1 MPDYLDDLRLAHVLADAADAATMDRFKALDLKVETKPDMTPVSEADKAAEELIRGHLSRA 60 M + DDLRLAHVLADAAD + RF+ALDL V+TKPD+TPV+E+D+ EE +RG LSRA Sbjct: 1 MASFDDDLRLAHVLADAADDLALKRFRALDLVVDTKPDLTPVTESDRLVEETLRGVLSRA 60 Query: 61 RPRDSVHGEEFGVAGTGPRRWVIDPIDGTKNYVRGVPVWATLIALMEAKEGGYQPVVGLV 120 RPRD+V GEE+G G R WVIDPIDGTKNYVRGVPVWATL+AL+E G +PVVGLV Sbjct: 61 RPRDAVVGEEYGKTGNSNRVWVIDPIDGTKNYVRGVPVWATLVALLE----GDRPVVGLV 116 Query: 121 SAPALGRRWWAVEDHGAFTGRSLTSAHRLHVSQVSTLSDASFAYSSLSGWEEQGRLDGFL 180 SAPAL RRWWA + G +TGR L A R HVS+VS L+DASF+YSSLSGWEE+G LD FL Sbjct: 117 SAPALHRRWWASKGGGTWTGRGLAKATRCHVSKVSELADASFSYSSLSGWEERGLLDSFL 176 Query: 181 DLTREVWRTRAYGDFWPYMMVAEGSVDLCAEPELSLWDMAANAIIVTEAGGTFTGLDGRP 240 LTR VWRTRAYGDFW ++MVAEG VD+ AEPELSLWD A II+ EAGG T L G Sbjct: 177 GLTRSVWRTRAYGDFWSHVMVAEGVVDVAAEPELSLWDAAPLPIILEEAGGRATNLRGEG 236 Query: 241 GPHSGNAAASNGRLHDELLGYLN 263 G SNG LHD L +LN Sbjct: 237 FEDGGPLVCSNGLLHDSALTWLN 259 Lambda K H 0.318 0.135 0.418 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: 283 Number of extensions: 11 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: 266 Length of database: 266 Length adjustment: 25 Effective length of query: 241 Effective length of database: 241 Effective search space: 58081 Effective search space used: 58081 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_017596874.1 D471_RS0100845 (histidinol-phosphatase)
to HMM TIGR02067 (hisN: histidinol-phosphatase (EC 3.1.3.15))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR02067.hmm # target sequence database: /tmp/gapView.27356.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02067 [M=252] Accession: TIGR02067 Description: his_9_HisN: histidinol-phosphatase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-88 282.9 0.0 1.3e-88 282.8 0.0 1.0 1 lcl|NCBI__GCF_000341125.1:WP_017596874.1 D471_RS0100845 histidinol-phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000341125.1:WP_017596874.1 D471_RS0100845 histidinol-phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 282.8 0.0 1.3e-88 1.3e-88 2 251 .. 8 258 .. 7 259 .. 0.97 Alignments for each domain: == domain 1 score: 282.8 bits; conditional E-value: 1.3e-88 TIGR02067 2 lalalelaeaageailkyfrasdlkvdkksdktpVteADraaEeaireliaakfPddgilGEEfgeeee 70 l+la+ la+aa++ lk+fra dl+vd+k+d tpVte+Dr +Ee++r ++++++P+d+++GEE+g+ ++ lcl|NCBI__GCF_000341125.1:WP_017596874.1 8 LRLAHVLADAADDLALKRFRALDLVVDTKPDLTPVTESDRLVEETLRGVLSRARPRDAVVGEEYGK-TG 75 6899*************************************************************6.67 PP TIGR02067 71 daeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallngge...re 136 ++++vWv+DPiDGTk+++rGvPvw+tL+aLle+++pv+G++s+Pal++r++a+kg+g+++ +g + lcl|NCBI__GCF_000341125.1:WP_017596874.1 76 NSNRVWVIDPIDGTKNYVRGVPVWATLVALLEGDRPVVGLVSAPALHRRWWASKGGGTWTGRGLakaTR 144 778********************************************************987434689* PP TIGR02067 137 lrvsevaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspy 205 +vs+v++l+dA+++++s + +e+++ + f l+r++++tr++gd++++++vA+G vd+++e+els++ lcl|NCBI__GCF_000341125.1:WP_017596874.1 145 CHVSKVSELADASFSYSSLSGWEERGLLDSFLGLTRSVWRTRAYGDFWSHVMVAEGVVDVAAEPELSLW 213 ********************************************************************* PP TIGR02067 206 DiaalipiieeAggvitdwkGkeaeeggeavaaanaalhdevlell 251 D a+l +i+eeAgg t+++G+ +e+gg +++n lhd++l l lcl|NCBI__GCF_000341125.1:WP_017596874.1 214 DAAPLPIILEEAGGRATNLRGEGFEDGGPL-VCSNGLLHDSALTWL 258 ****************************99.9**********9877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (252 nodes) Target sequences: 1 (266 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.15 // [ok]
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