Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate Dsui_1410 Dsui_1410 ATP phosphoribosyltransferase
Query= reanno::HerbieS:HSERO_RS20350 (216 letters) >FitnessBrowser__PS:Dsui_1410 Length = 216 Score = 328 bits (841), Expect = 5e-95 Identities = 165/208 (79%), Positives = 185/208 (88%) Query: 5 LTLALSKGRIFEETLPLLKAAGITVSEDPESSRKLILPTNDPDVRVIIVRASDVPTYVQY 64 +T+ALSKGRIFEETLPLL AAGI +E+PE+SRKLI+ TN PDVRV+IVRA+D PTYVQ+ Sbjct: 4 ITIALSKGRIFEETLPLLAAAGIVPAENPETSRKLIIGTNRPDVRVVIVRATDAPTYVQH 63 Query: 65 GAADFGVAGKDVLLEHGGEGLYQPIDLNIAKCRLSVAVQEGFDYANAVRQGARLRVVTKY 124 GAAD GV GKDVL+EHGG GLYQP+DL IAKCR+SVAV GFDY +AVRQGARL++ TKY Sbjct: 64 GAADLGVVGKDVLIEHGGAGLYQPLDLKIAKCRMSVAVPAGFDYEHAVRQGARLKIATKY 123 Query: 125 VNTAREHFAAKGVHVDLIKLYGSMELGPLVGLSDAIVDLVSTGGTLRANKLVEVEHIIDI 184 AREHFAAKGVHVDLIKLYGSMEL PL GLSDAIVDLVSTGGTL+AN LVEVEHI+DI Sbjct: 124 TKIAREHFAAKGVHVDLIKLYGSMELAPLAGLSDAIVDLVSTGGTLKANNLVEVEHIMDI 183 Query: 185 SSRLVVNQAALKLKRERLQPILDAFEKA 212 SSRL+VNQA+LKLKRE L PILDAF +A Sbjct: 184 SSRLIVNQASLKLKREILGPILDAFTQA 211 Lambda K H 0.318 0.136 0.373 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: 219 Number of extensions: 2 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: 216 Length of database: 216 Length adjustment: 22 Effective length of query: 194 Effective length of database: 194 Effective search space: 37636 Effective search space used: 37636 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: 45 (21.9 bits)
Align candidate Dsui_1410 Dsui_1410 (ATP phosphoribosyltransferase)
to HMM TIGR00070 (hisG: ATP phosphoribosyltransferase (EC 2.4.2.17))
# 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/TIGR00070.hmm # target sequence database: /tmp/gapView.9480.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00070 [M=183] Accession: TIGR00070 Description: hisG: ATP phosphoribosyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-64 201.8 0.1 5.2e-64 201.6 0.1 1.0 1 lcl|FitnessBrowser__PS:Dsui_1410 Dsui_1410 ATP phosphoribosyltran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_1410 Dsui_1410 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 201.6 0.1 5.2e-64 5.2e-64 1 183 [] 4 189 .. 4 189 .. 0.94 Alignments for each domain: == domain 1 score: 201.6 bits; conditional E-value: 5.2e-64 TIGR00070 1 lriAlpKGrleeetlkllekaglklskke..erkliasaedeevevlllrakdiptyvekgaadlGitGkDlleEse 75 ++iAl KGr++eetl ll++ag+ ++ +rkli+ +++++v+v+++ra+d ptyv++gaadlG++GkD+l E++ lcl|FitnessBrowser__PS:Dsui_1410 4 ITIALSKGRIFEETLPLLAAAGIVPAENPetSRKLIIGTNRPDVRVVIVRATDAPTYVQHGAADLGVVGKDVLIEHG 80 79********************9977766689*******************************************77 PP TIGR00070 76 ad.vvelldlgfgkcklvlAvpeesdvesledlkegk..riATkypnltreylekkgvkveivkleGavElapllgl 149 + +++ ldl++ kc++++Avp d+e++ +++g+ +iATky++++re+++ kgv+v+++kl+G++Elapl+gl lcl|FitnessBrowser__PS:Dsui_1410 81 GAgLYQPLDLKIAKCRMSVAVPAGFDYEHA--VRQGArlKIATKYTKIAREHFAAKGVHVDLIKLYGSMELAPLAGL 155 666************************994..4444346************************************** PP TIGR00070 150 adaIvDivetGttLrengLkiieeilessarlia 183 +daIvD+v+tG tL++n+L+++e+i+++s+rli+ lcl|FitnessBrowser__PS:Dsui_1410 156 SDAIVDLVSTGGTLKANNLVEVEHIMDISSRLIV 189 ********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (216 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: 6.75 // [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