Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate 209044 DVU0114 ATP phosphoribosyltransferase
Query= reanno::DvH:209044 (293 letters) >MicrobesOnline__882:209044 Length = 293 Score = 579 bits (1492), Expect = e-170 Identities = 293/293 (100%), Positives = 293/293 (100%) Query: 1 MSIRTPMKLGIPKGSLEEATINLLARSGWKIRKHHRNYFPEINDPELTARLCRVQEIPRY 60 MSIRTPMKLGIPKGSLEEATINLLARSGWKIRKHHRNYFPEINDPELTARLCRVQEIPRY Sbjct: 1 MSIRTPMKLGIPKGSLEEATINLLARSGWKIRKHHRNYFPEINDPELTARLCRVQEIPRY 60 Query: 61 IEDGILDVGLTGKDWLLETGSDVVVVSDLVYSKVSNRPARWVLAVAGDSPYTRPEDLAGK 120 IEDGILDVGLTGKDWLLETGSDVVVVSDLVYSKVSNRPARWVLAVAGDSPYTRPEDLAGK Sbjct: 61 IEDGILDVGLTGKDWLLETGSDVVVVSDLVYSKVSNRPARWVLAVAGDSPYTRPEDLAGK 120 Query: 121 RIATELLGVTKRYFADAGIEVNVQYSWGATEAKVVEGLADAIVEVTETGTTIKAHGLRII 180 RIATELLGVTKRYFADAGIEVNVQYSWGATEAKVVEGLADAIVEVTETGTTIKAHGLRII Sbjct: 121 RIATELLGVTKRYFADAGIEVNVQYSWGATEAKVVEGLADAIVEVTETGTTIKAHGLRII 180 Query: 181 SEVLLTNTVLIANRAAWEDPCRRRKIEQIDLLLQGALRADSLVGLKMNVPTRCLDAVLDQ 240 SEVLLTNTVLIANRAAWEDPCRRRKIEQIDLLLQGALRADSLVGLKMNVPTRCLDAVLDQ Sbjct: 181 SEVLLTNTVLIANRAAWEDPCRRRKIEQIDLLLQGALRADSLVGLKMNVPTRCLDAVLDQ 240 Query: 241 LPSLNSPTVAGLRDNTWFAVEIVVDNGVVRDLIPRLREAGAEGIIEYALNKVI 293 LPSLNSPTVAGLRDNTWFAVEIVVDNGVVRDLIPRLREAGAEGIIEYALNKVI Sbjct: 241 LPSLNSPTVAGLRDNTWFAVEIVVDNGVVRDLIPRLREAGAEGIIEYALNKVI 293 Lambda K H 0.319 0.137 0.402 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: 448 Number of extensions: 19 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: 293 Length of database: 293 Length adjustment: 26 Effective length of query: 267 Effective length of database: 267 Effective search space: 71289 Effective search space used: 71289 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate 209044 DVU0114 (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.29437.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-55 173.1 0.0 3.4e-55 172.8 0.0 1.1 1 lcl|MicrobesOnline__882:209044 DVU0114 ATP phosphoribosyltransf Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:209044 DVU0114 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 172.8 0.0 3.4e-55 3.4e-55 1 183 [] 7 192 .. 7 192 .. 0.98 Alignments for each domain: == domain 1 score: 172.8 bits; conditional E-value: 3.4e-55 TIGR00070 1 lriAlpKGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDlleEseadvv 79 +++++pKG+lee t++ll+++g+k++k++ r+++ +++d+e+++ l+r ++ip+y+e+g++d+G+tGkD+l E ++dvv lcl|MicrobesOnline__882:209044 7 MKLGIPKGSLEEATINLLARSGWKIRKHH-RNYFPEINDPELTARLCRVQEIPRYIEDGILDVGLTGKDWLLETGSDVV 84 689**************************.************************************************* PP TIGR00070 80 elldlgfgkc.....klvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkleGavElapllgladaI 153 + dl ++k ++vlAv +s+++++edl+ gkriAT+ +t++y+++ g++v++ ++Ga+E++++ gladaI lcl|MicrobesOnline__882:209044 85 VVSDLVYSKVsnrpaRWVLAVAGDSPYTRPEDLA-GKRIATELLGVTKRYFADAGIEVNVQYSWGATEAKVVEGLADAI 162 *****9988777777*******************.9******************************************* PP TIGR00070 154 vDivetGttLrengLkiieeilessarlia 183 v ++etGtt++++gL+ii+e+l ++++lia lcl|MicrobesOnline__882:209044 163 VEVTETGTTIKAHGLRIISEVLLTNTVLIA 192 ****************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (293 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: 8.63 // [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