Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate SMa0483 SMa0483 Phosphatase
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >FitnessBrowser__Smeli:SMa0483 Length = 308 Score = 218 bits (555), Expect = 1e-61 Identities = 111/231 (48%), Positives = 140/231 (60%), Gaps = 4/231 (1%) Query: 29 RTPVAVDDKADASPVTIADREAERTIRAIIEAERPDDGIYGEEFGTKNLDAEWVWVIDPI 88 R P+A K+DASPVT DR E+ +R I PD G+ GEEFG + L E+VWVIDPI Sbjct: 82 REPIA---KSDASPVTETDRAVEKCLRERIADHFPDHGVLGEEFGAEGLGNEFVWVIDPI 138 Query: 89 DGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPIVRDRWLGVEGRPTLFNGQPARVRECA 148 DGTK+F+ G P++GTLI+L G P+LG+ID P+ DRWLGV G+PT N P R Sbjct: 139 DGTKAFVAGLPVYGTLISLTRGGTPILGLIDNPMTGDRWLGVSGQPTTLNNVPIRTASTT 198 Query: 149 GGLAAATLGTTSPDLFPGADQDAFRRVAGAAKVSVYGGDCYSYGLLAAGYYDLVVESGLK 208 LA A + +PD F AD+ + + VYGG C +YG +A G D+ ++ GL Sbjct: 199 -ALATAFIANGNPDAFSPADKSRVESLRRITRWCVYGGSCIAYGRVADGSVDISIDGGLD 257 Query: 209 LYDFAALVPVVTGAGGLMTDWDGRPLDATSSGRVVAAGDARTHRETLAALA 259 YD+ ALVPV+TGAGG +TDW GRPL S G VA HR L LA Sbjct: 258 PYDYCALVPVITGAGGCITDWQGRPLTLNSGGLCVATATDLLHRHVLEILA 308 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: 304 Number of extensions: 13 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: 308 Length adjustment: 26 Effective length of query: 234 Effective length of database: 282 Effective search space: 65988 Effective search space used: 65988 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 SMa0483 SMa0483 (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.18453.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-94 301.6 0.0 2.6e-94 301.4 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMa0483 SMa0483 Phosphatase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMa0483 SMa0483 Phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 301.4 0.0 2.6e-94 2.6e-94 2 251 .. 60 307 .. 59 308 .] 0.98 Alignments for each domain: == domain 1 score: 301.4 bits; conditional E-value: 2.6e-94 TIGR02067 2 lalalelaeaageailkyfrasdlkvdkksdktpVteADraaEeaireliaakfPddgilGEEfgeeeedaeyvWv 77 +++a+++a++a+++i ++ + +++ +k++++ pVte+Dra+E+++re ia++fPd+g+lGEEfg+e ++e+vWv lcl|FitnessBrowser__Smeli:SMa0483 60 ASFAHDIADLARQTISSAAGVRREPIAKSDAS-PVTETDRAVEKCLRERIADHFPDHGVLGEEFGAEGLGNEFVWV 134 689******************99999988777.******************************************* PP TIGR02067 78 lDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallnggerelrvsevaklsdAvlvtt 153 +DPiDGTk+F++G+Pv+gtLi+L+++g+p+lG+i++P++g+r+++++g+ ++ln+ +++r++++++l++A+++++ lcl|FitnessBrowser__Smeli:SMa0483 135 IDPIDGTKAFVAGLPVYGTLISLTRGGTPILGLIDNPMTGDRWLGVSGQPTTLNN--VPIRTASTTALATAFIANG 208 *****************************************************96..9****************** PP TIGR02067 154 spkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDiaalipiieeAggvitdwkGkea 229 +p +++++++++++e+lrr +r+++ygg+c+ay vA+G+vd+ ++ +l+pyD++al+p+i++Agg+itdw+G+++ lcl|FitnessBrowser__Smeli:SMa0483 209 NP-DAFSPADKSRVESLRRITRWCVYGGSCIAYGRVADGSVDISIDGGLDPYDYCALVPVITGAGGCITDWQGRPL 283 **.7999********************************************************************9 PP TIGR02067 230 e..eggeavaaanaalhdevlell 251 + +gg +va+a++ lh++vle+l lcl|FitnessBrowser__Smeli:SMa0483 284 TlnSGGLCVATATDLLHRHVLEIL 307 998999****************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (252 nodes) Target sequences: 1 (308 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: 9.35 // [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