Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate 3609389 Dshi_2774 histidinol-phosphate phosphatase, putative (RefSeq)
Query= reanno::Phaeo:GFF2154 (250 letters) >FitnessBrowser__Dino:3609389 Length = 273 Score = 310 bits (795), Expect = 1e-89 Identities = 160/249 (64%), Positives = 186/249 (74%), Gaps = 1/249 (0%) Query: 1 MADAARQAILPYFRSAGLQSDNKLD-EGFDPVTIADRAAEQAMRSVLSELRPEDSILGEE 59 +A AAR L FR GL +NK FDPVT ADRAAE+AMR +L+ RP+D ILGEE Sbjct: 22 LAQAARGPTLAQFRQHGLGIENKAGVAAFDPVTEADRAAERAMRDLLAVERPDDGILGEE 81 Query: 60 FGETHGQSGRTWVLDPIDGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIGERFIGTP 119 +G G SG TWVLDPIDGTR ++SGTPTWGVLIAL D DGP +GI+DQPY ERF+G Sbjct: 82 YGAQAGTSGLTWVLDPIDGTRAYMSGTPTWGVLIALSDRDGPRIGIIDQPYTAERFMGGA 141 Query: 120 EGASLTGPLGHSALVTRATDSLSEATLFTTFPEVGTEAERAAFQRVSAQVRLTRYGMDCY 179 A L GP G L TR LSEAT+FTTFPE+GT AERA F+ V+ RLTR+GMDCY Sbjct: 142 GRARLDGPHGSLPLATRRVAGLSEATVFTTFPEIGTAAERAGFEAVARVCRLTRFGMDCY 201 Query: 180 AYALLAAGQCDLVIEAGLNAYDIQAPIAVIQAAGGVVTNWQGEPAHEGGQVLAAATAELH 239 AY LLAAGQ DLVIEAGL YDI APIAVI+AAGG+VT+WQG PAH GG+VLAA E+H Sbjct: 202 AYGLLAAGQIDLVIEAGLQPYDICAPIAVIEAAGGIVTDWQGGPAHGGGRVLAAGGPEVH 261 Query: 240 AAALALIQQ 248 AAAL ++++ Sbjct: 262 AAALEILRK 270 Lambda K H 0.317 0.134 0.392 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: 12 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: 250 Length of database: 273 Length adjustment: 25 Effective length of query: 225 Effective length of database: 248 Effective search space: 55800 Effective search space used: 55800 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 3609389 Dshi_2774 (histidinol-phosphate phosphatase, putative (RefSeq))
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.10325.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-87 277.5 0.1 5.9e-87 277.3 0.1 1.0 1 lcl|FitnessBrowser__Dino:3609389 Dshi_2774 histidinol-phosphate p Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3609389 Dshi_2774 histidinol-phosphate phosphatase, putative (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 277.3 0.1 5.9e-87 5.9e-87 3 251 .. 17 268 .. 15 269 .. 0.98 Alignments for each domain: == domain 1 score: 277.3 bits; conditional E-value: 5.9e-87 TIGR02067 3 alalelaeaageailkyfrasdlkvdkksdk...tpVteADraaEeaireliaakfPddgilGEEfgeeeedaeyvW 76 ++a++la+aa+ +l fr++ l ++k+ +pVteADraaE+a+r+l+a ++PddgilGEE+g+++++++ +W lcl|FitnessBrowser__Dino:3609389 17 QVAEALAQAARGPTLAQFRQHGLGIENKAGVaafDPVTEADRAAERAMRDLLAVERPDDGILGEEYGAQAGTSGLTW 93 6899*******************99999988899******************************************* PP TIGR02067 77 vlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallng.gerelrvsevaklsdAvlvt 152 vlDPiDGT+++++G P wg+LiaL + + p +G+i+qP++ erf++ +g++ l + g+ +l++++va ls+A+++t lcl|FitnessBrowser__Dino:3609389 94 VLDPIDGTRAYMSGTPTWGVLIALSDRDGPRIGIIDQPYTAERFMGGAGRARLDGPhGSLPLATRRVAGLSEATVFT 170 *****************************************************998666****************** PP TIGR02067 153 tspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDiaalipiieeAggvitdwkGkea 229 t p ++ + +er+ fe+++r +rltr+g dcyay l+A+G++dlv+ea+l+pyDi+a i +ie Agg++tdw+G +a lcl|FitnessBrowser__Dino:3609389 171 TFP-EIGTAAERAGFEAVARVCRLTRFGMDCYAYGLLAAGQIDLVIEAGLQPYDICAPIAVIEAAGGIVTDWQGGPA 246 ***.8************************************************************************ PP TIGR02067 230 eeggeavaaanaalhdevlell 251 + gg+++aa+ +++h+++le+l lcl|FitnessBrowser__Dino:3609389 247 HGGGRVLAAGGPEVHAAALEIL 268 ********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (252 nodes) Target sequences: 1 (273 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.70 // [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