Align Histidinol-phosphatase; HolPase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate WP_037573048.1 BS73_RS15920 histidinol-phosphatase
Query= SwissProt::Q9K4B1 (266 letters) >NCBI__GCF_000744815.1:WP_037573048.1 Length = 264 Score = 400 bits (1028), Expect = e-116 Identities = 196/263 (74%), Positives = 221/263 (84%) Query: 1 MPDYLDDLRLAHVLADAADAATMDRFKALDLKVETKPDMTPVSEADKAAEELIRGHLSRA 60 MPD+ DDLRLAHVLAD AD+ T +RFKALDL+VETKPD+TPVS+ADKAAE+++R LSRA Sbjct: 1 MPDFHDDLRLAHVLADHADSVTTERFKALDLRVETKPDLTPVSDADKAAEDVVRSVLSRA 60 Query: 61 RPRDSVHGEEFGVAGTGPRRWVIDPIDGTKNYVRGVPVWATLIALMEAKEGGYQPVVGLV 120 RPRD+V GEE GV G GPRRWVIDPIDGTKNYVRGVPVWATLI+L+E GG +PVVGLV Sbjct: 61 RPRDAVMGEEHGVTGHGPRRWVIDPIDGTKNYVRGVPVWATLISLLELGPGGEEPVVGLV 120 Query: 121 SAPALGRRWWAVEDHGAFTGRSLTSAHRLHVSQVSTLSDASFAYSSLSGWEEQGRLDGFL 180 SAPALG+RWW+ + GAFTGRSL A RL VS VS LSDAS +YSSL+GWEE+G L F+ Sbjct: 121 SAPALGKRWWSAKGSGAFTGRSLARATRLQVSDVSRLSDASLSYSSLTGWEERGLLPNFV 180 Query: 181 DLTREVWRTRAYGDFWPYMMVAEGSVDLCAEPELSLWDMAANAIIVTEAGGTFTGLDGRP 240 DL+R+VWRTRA+GDFW YMMVAEG+VDL AEPELSLWDMAA IVTEAGG FT L GRP Sbjct: 181 DLSRKVWRTRAFGDFWSYMMVAEGAVDLAAEPELSLWDMAAPCAIVTEAGGRFTDLQGRP 240 Query: 241 GPHSGNAAASNGRLHDELLGYLN 263 G H NA ASNG LH+ LLG LN Sbjct: 241 GVHGPNAVASNGLLHEALLGSLN 263 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: 297 Number of extensions: 8 Number of successful extensions: 1 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: 264 Length adjustment: 25 Effective length of query: 241 Effective length of database: 239 Effective search space: 57599 Effective search space used: 57599 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_037573048.1 BS73_RS15920 (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.4059402.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-88 280.8 0.0 5.8e-88 280.6 0.0 1.0 1 NCBI__GCF_000744815.1:WP_037573048.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037573048.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 280.6 0.0 5.8e-88 5.8e-88 2 251 .. 8 262 .. 7 263 .. 0.95 Alignments for each domain: == domain 1 score: 280.6 bits; conditional E-value: 5.8e-88 TIGR02067 2 lalalelaeaageailkyfrasdlkvdkksdktpVteADraaEeaireliaakfPddgilGEEfgeeeedaey 74 l+la+ la+ a+++++++f+a dl v++k+d tpV++AD+aaE+++r+++++++P+d+++GEE+g +++ + NCBI__GCF_000744815.1:WP_037573048.1 8 LRLAHVLADHADSVTTERFKALDLRVETKPDLTPVSDADKAAEDVVRSVLSRARPRDAVMGEEHGV-TGHGPR 79 6899*************************************************************5.78889* PP TIGR02067 75 vWvlDPiDGTksFirGvPvwgtLiaLlekgk....pvlGvisqPalgerfvaakgegallngge...relrvs 140 +Wv+DPiDGTk+++rGvPvw+tLi+Lle g pv+G++s+Palg+r+++akg+ga++ ++ +l+vs NCBI__GCF_000744815.1:WP_037573048.1 80 RWVIDPIDGTKNYVRGVPVWATLISLLELGPggeePVVGLVSAPALGKRWWSAKGSGAFTGRSLaraTRLQVS 152 ***************************96544445*************************87335789***** PP TIGR02067 141 evaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDiaalipi 213 v++lsdA+l+++s + +e+++ +f +l rk+++tr++gd+++y++vA+G+vdl++e+els++D+aa i NCBI__GCF_000744815.1:WP_037573048.1 153 DVSRLSDASLSYSSLTGWEERGLLPNFVDLSRKVWRTRAFGDFWSYMMVAEGAVDLAAEPELSLWDMAAPCAI 225 ************************************************************************* PP TIGR02067 214 ieeAggvitdwkGkeaeeggeavaaanaalhdevlell 251 ++eAgg +td++G++ +g +a +a+n lh+++l +l NCBI__GCF_000744815.1:WP_037573048.1 226 VTEAGGRFTDLQGRPGVHGPNA-VASNGLLHEALLGSL 262 **********************.999*******99887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (252 nodes) Target sequences: 1 (264 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 12.89 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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