Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_004307358.1 C665_RS09760 ATP phosphoribosyltransferase
Query= reanno::HerbieS:HSERO_RS20350 (216 letters) >NCBI__GCF_000310185.1:WP_004307358.1 Length = 214 Score = 320 bits (820), Expect = 1e-92 Identities = 161/208 (77%), Positives = 182/208 (87%) Query: 5 LTLALSKGRIFEETLPLLKAAGITVSEDPESSRKLILPTNDPDVRVIIVRASDVPTYVQY 64 +TLALSKGRIFEETLPLL AAGI +++PESSRKLI+ TN PDVR++IVRA+D PTYVQY Sbjct: 4 ITLALSKGRIFEETLPLLAAAGIVPTDNPESSRKLIIGTNRPDVRLVIVRATDTPTYVQY 63 Query: 65 GAADFGVAGKDVLLEHGGEGLYQPIDLNIAKCRLSVAVQEGFDYANAVRQGARLRVVTKY 124 GAAD G+AGKDVL+EHGG GLYQP+DL IAKCRL VAVQ+GFDYA A R G R+RV TKY Sbjct: 64 GAADLGIAGKDVLVEHGGAGLYQPLDLEIAKCRLCVAVQKGFDYAAATRPGGRIRVATKY 123 Query: 125 VNTAREHFAAKGVHVDLIKLYGSMELGPLVGLSDAIVDLVSTGGTLRANKLVEVEHIIDI 184 +N A+ HFA KG+HVDLIKLYGSMEL PLVGL+DAIVDLVSTGGTLRAN L EVE I+ I Sbjct: 124 MNAAKAHFAGKGMHVDLIKLYGSMELAPLVGLADAIVDLVSTGGTLRANNLEEVEDIMPI 183 Query: 185 SSRLVVNQAALKLKRERLQPILDAFEKA 212 SSRL+VNQA+LKLKRE LQP+LDAF A Sbjct: 184 SSRLIVNQASLKLKRELLQPVLDAFAGA 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: 208 Number of extensions: 3 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: 214 Length adjustment: 22 Effective length of query: 194 Effective length of database: 192 Effective search space: 37248 Effective search space used: 37248 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 WP_004307358.1 C665_RS09760 (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.1172818.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-62 194.6 0.0 8.1e-62 194.4 0.0 1.0 1 NCBI__GCF_000310185.1:WP_004307358.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000310185.1:WP_004307358.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 194.4 0.0 8.1e-62 8.1e-62 1 183 [] 4 189 .. 4 189 .. 0.95 Alignments for each domain: == domain 1 score: 194.4 bits; conditional E-value: 8.1e-62 TIGR00070 1 lriAlpKGrleeetlkllekaglklskke..erkliasaedeevevlllrakdiptyvekgaadlGitGkDll 71 +++Al KGr++eetl ll++ag+ +++ +rkli+ +++++v+++++ra+d ptyv++gaadlGi GkD+l NCBI__GCF_000310185.1:WP_004307358.1 4 ITLALSKGRIFEETLPLLAAAGIVPTDNPesSRKLIIGTNRPDVRLVIVRATDTPTYVQYGAADLGIAGKDVL 76 799********************987776689***************************************** PP TIGR00070 72 eEsead.vvelldlgfgkcklvlAvpeesdvesledlkegk.riATkypnltreylekkgvkveivkleGavE 142 E++ + +++ ldl++ kc+l++Av++ d+ +++ g+ r+ATky n ++++++ kg++v+++kl+G++E NCBI__GCF_000310185.1:WP_004307358.1 77 VEHGGAgLYQPLDLEIAKCRLCVAVQKGFDYAAATRPG-GRiRVATKYMNAAKAHFAGKGMHVDLIKLYGSME 148 **77666**********************999844444.668******************************* PP TIGR00070 143 lapllgladaIvDivetGttLrengLkiieeilessarlia 183 lapl+gladaIvD+v+tG tLr+n+L+++e+i+ +s+rli+ NCBI__GCF_000310185.1:WP_004307358.1 149 LAPLVGLADAIVDLVSTGGTLRANNLEEVEDIMPISSRLIV 189 ***************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (214 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: 18.84 // [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