Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_011386518.1 AMB_RS21100 histidinol-phosphatase
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >NCBI__GCF_000009985.1:WP_011386518.1 Length = 258 Score = 318 bits (816), Expect = 5e-92 Identities = 158/254 (62%), Positives = 189/254 (74%), Gaps = 1/254 (0%) Query: 5 CPTPLVTLAERLADASGPVIRQYFRTPVAVDDKADASPVTIADREAERTIRAIIEAERPD 64 CP+ + LAE+LADA+ PV+R+YFRTPVAVDDKAD+SPVTIADRE E +RAI+ AE P Sbjct: 4 CPSEFIALAEKLADAARPVVRKYFRTPVAVDDKADSSPVTIADREVEAAMRAILAAEAPS 63 Query: 65 DGIYGEEFGTKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPIVR 124 GI GEE G +N DAE+VWV+DPIDGT +FITG+P FGTLI+L G P+LG+IDQ Sbjct: 64 HGILGEEHGRENCDAEYVWVLDPIDGTAAFITGKPSFGTLISLARNGTPILGLIDQAFTN 123 Query: 125 DRWLGVEGRPTLFNGQPARVRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAAKVSVY 184 +RWLG GRPT NGQPARVR C LA A TT+P+LF A + A+ R+A K Y Sbjct: 124 ERWLGALGRPTTLNGQPARVRACP-DLAHAYAFTTAPELFCEATRPAWDRIAAGCKRPRY 182 Query: 185 GGDCYSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLDATSSGRVVA 244 G DCY+Y LL++G+ DLVVE+GLK YDFAALVPVV GAGG+MTDW G+PL S G+V A Sbjct: 183 GCDCYAYALLSSGFCDLVVEAGLKPYDFAALVPVVEGAGGIMTDWSGKPLTIHSDGKVCA 242 Query: 245 AGDARTHRETLAAL 258 AGD R H E L L Sbjct: 243 AGDRRLHAEALGVL 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: 305 Number of extensions: 15 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: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 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)
Align candidate WP_011386518.1 AMB_RS21100 (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.27740.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-93 297.4 0.0 5e-93 297.2 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386518.1 AMB_RS21100 histidinol-phosphata Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011386518.1 AMB_RS21100 histidinol-phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 297.2 0.0 5e-93 5e-93 3 251 .. 10 256 .. 8 257 .. 0.97 Alignments for each domain: == domain 1 score: 297.2 bits; conditional E-value: 5e-93 TIGR02067 3 alalelaeaageailkyfrasdlkvdkksdktpVteADraaEeaireliaakfPddgilGEEfgeeeed 71 ala++la+aa+ ++ kyfr+ ++vd k+d++pVt+ADr++E+a+r+++aa+ P++gilGEE+g e+ d lcl|NCBI__GCF_000009985.1:WP_011386518.1 10 ALAEKLADAARPVVRKYFRT-PVAVDDKADSSPVTIADREVEAAMRAILAAEAPSHGILGEEHGRENCD 77 799****************9.77888889999************************************* PP TIGR02067 72 aeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallnggerelrvs 140 aeyvWvlDPiDGT +Fi+G P +gtLi+L+++g+p+lG+i+q +++er+++a g+ ++lng +++rv+ lcl|NCBI__GCF_000009985.1:WP_011386518.1 78 AEYVWVLDPIDGTAAFITGKPSFGTLISLARNGTPILGLIDQAFTNERWLGALGRPTTLNG--QPARVR 144 ************************************************************8..8***** PP TIGR02067 141 evaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDiaa 209 ++ +l++A+ +tt p +l+ e++r a++++++ +++ ryg+dcyayal+ sG+ dlvvea+l+pyD+aa lcl|NCBI__GCF_000009985.1:WP_011386518.1 145 ACPDLAHAYAFTTAP-ELFCEATRPAWDRIAAGCKRPRYGCDCYAYALLSSGFCDLVVEAGLKPYDFAA 212 ***************.79999************************************************ PP TIGR02067 210 lipiieeAggvitdwkGkeae..eggeavaaanaalhdevlell 251 l+p++e+Agg++tdw+Gk+++ ++g++ aa++++lh+e+l +l lcl|NCBI__GCF_000009985.1:WP_011386518.1 213 LVPVVEGAGGIMTDWSGKPLTihSDGKVCAAGDRRLHAEALGVL 256 *******************999899***************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (252 nodes) Target sequences: 1 (258 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 6.98 // [ok]
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