Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_029000578.1 H537_RS0128475 ATP phosphoribosyltransferase
Query= reanno::BFirm:BPHYT_RS17715 (232 letters) >NCBI__GCF_000430725.1:WP_029000578.1 Length = 225 Score = 317 bits (813), Expect = 9e-92 Identities = 167/212 (78%), Positives = 183/212 (86%), Gaps = 4/212 (1%) Query: 17 LTLALSKGRIFEETLPLLAAAGIEVAEDPETSRKLILPTTDANLRVIIVRATDVPTYVEY 76 +TLALSKGRIFEETLPLL AAGIEV EDPE SRKLILPT +RV++VRATDVPTYV+Y Sbjct: 5 ITLALSKGRIFEETLPLLRAAGIEVGEDPEKSRKLILPTNRPEVRVVLVRATDVPTYVQY 64 Query: 77 GAADFGVAGKDVLLEHGG----SGLYQPVDLDIARCRMSVAVAAGFDYANAVRQGARLRV 132 G AD GVAG DVLLEH G +GLYQP+DL IA CRMSVAV A FDY AVRQG+R+RV Sbjct: 65 GGADLGVAGLDVLLEHAGGETATGLYQPLDLRIASCRMSVAVRADFDYEAAVRQGSRIRV 124 Query: 133 ATKYVETAREHFAAKGVHVDLIKLYGSMELAPLVGLADAIVDLVSSGNTLRANNLVEVEE 192 ATKY AR+HFA KGVHVDLIKLYGSMELAPL GLADAIVDLVS+G+TLRANNLVEVE+ Sbjct: 125 ATKYTHIARQHFADKGVHVDLIKLYGSMELAPLTGLADAIVDLVSTGSTLRANNLVEVEQ 184 Query: 193 IMQISSRLVVNQAALKLKRAALRPILDAFERA 224 IM ISSRLVVNQAALKLKRAAL+P++DAF A Sbjct: 185 IMPISSRLVVNQAALKLKRAALKPLIDAFAGA 216 Lambda K H 0.318 0.132 0.357 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: 211 Number of extensions: 4 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: 232 Length of database: 225 Length adjustment: 23 Effective length of query: 209 Effective length of database: 202 Effective search space: 42218 Effective search space used: 42218 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: 46 (22.3 bits)
Align candidate WP_029000578.1 H537_RS0128475 (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.2375134.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-62 196.2 0.0 2.7e-62 196.0 0.0 1.0 1 NCBI__GCF_000430725.1:WP_029000578.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000430725.1:WP_029000578.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 196.0 0.0 2.7e-62 2.7e-62 1 183 [] 5 194 .. 5 194 .. 0.93 Alignments for each domain: == domain 1 score: 196.0 bits; conditional E-value: 2.7e-62 TIGR00070 1 lriAlpKGrleeetlkllekaglklskke..erkliasaedeevevlllrakdiptyvekgaadlGitGkDll 71 +++Al KGr++eetl ll++ag+++ + +rkli ++++ev+v+l+ra+d+ptyv++g adlG+ G D+l NCBI__GCF_000430725.1:WP_029000578.1 5 ITLALSKGRIFEETLPLLRAAGIEVGEDPekSRKLILPTNRPEVRVVLVRATDVPTYVQYGGADLGVAGLDVL 77 799*********************98876689***************************************** PP TIGR00070 72 eE...sead....vvelldlgfgkcklvlAvpeesdvesledlkegk..riATkypnltreylekkgvkveiv 135 E + +++ ldl++ c++++Av+ + d+e+ ++++g+ r+ATky++++r+++++kgv+v+++ NCBI__GCF_000430725.1:WP_029000578.1 78 LEhagG--EtatgLYQPLDLRIASCRMSVAVRADFDYEA--AVRQGSriRVATKYTHIARQHFADKGVHVDLI 146 **6541..14567************************99..55554447************************ PP TIGR00070 136 kleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183 kl+G++Elapl+gladaIvD+v+tG+tLr+n+L+++e+i+ +s+rl++ NCBI__GCF_000430725.1:WP_029000578.1 147 KLYGSMELAPLTGLADAIVDLVSTGSTLRANNLVEVEQIMPISSRLVV 194 *********************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (225 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: 14.60 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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