Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_012853319.1 TCUR_RS14760 ATP phosphoribosyltransferase
Query= reanno::Miya:8501229 (293 letters) >NCBI__GCF_000024385.1:WP_012853319.1 Length = 291 Score = 236 bits (601), Expect = 6e-67 Identities = 132/291 (45%), Positives = 195/291 (67%), Gaps = 4/291 (1%) Query: 6 MLKIGIPKGSLEEATVNLFARSGWKIRKHH-RNYFPEINDPELT-ARLCRVQEIPRYLED 63 ML + +PKGSLE+AT+ LF + +R+ R+Y I+DP + R+ R QEIP Y+E Sbjct: 1 MLSLVLPKGSLEKATMELFDAADLTVRRSSDRDYRASIDDPRIDRVRVLRPQEIPTYIEQ 60 Query: 64 GVLDVGLTGKDWLLETGADVVTVSDLVYSKVSNRPARWVLAVAGDSPYVRPEDLA-GCTI 122 G+ D+G+TG+DW+ ET +DVV++ L YSK ++ P R V+AV D+P+ + DL G I Sbjct: 61 GLFDLGITGRDWITETDSDVVSLGQLQYSKATSNPVRVVMAVPKDAPWQKVSDLPEGVRI 120 Query: 123 ATELLGVTRRYFEDAGIPVKVQYSWGATEAKVVEGLADAIVEVTETGTTIKAHGLRIIAE 182 +TE +T+R+ E G+ V S+GATEAKV + + DAIV++TETG++++ +GLRI+ Sbjct: 121 STEFPSLTQRFLEKHGVKATVVPSYGATEAKVPD-IVDAIVDLTETGSSLRKNGLRILDT 179 Query: 183 VLLTNTVLIAGKAAWADPWKRAKIEQIDLLLQGALRADSLVGLKMNVPAHNLDAVLDQLP 242 +L + T L+A + ++ D KRA +E I LLLQGA+RA V LK+NV A +L AVLD +P Sbjct: 180 LLTSYTELVANRQSYEDEAKRAAMEDIALLLQGAIRARGNVLLKLNVSAADLQAVLDIMP 239 Query: 243 SLNSPTVAGLRDSTWYAVEIVVENDLVRDLIPRLRAAGAEGIIEYSLNKVI 293 +++SPTV L +AVE VV V LIP L+AAGA I+E ++K++ Sbjct: 240 AMSSPTVTSLAGGEAHAVESVVAKKGVNTLIPALKAAGARDILEIPISKIV 290 Lambda K H 0.318 0.136 0.401 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: 241 Number of extensions: 14 Number of successful extensions: 4 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: 291 Length adjustment: 26 Effective length of query: 267 Effective length of database: 265 Effective search space: 70755 Effective search space used: 70755 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: 48 (23.1 bits)
Align candidate WP_012853319.1 TCUR_RS14760 (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.20655.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-58 182.5 0.0 4.8e-58 182.1 0.0 1.1 1 lcl|NCBI__GCF_000024385.1:WP_012853319.1 TCUR_RS14760 ATP phosphoribosylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024385.1:WP_012853319.1 TCUR_RS14760 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 182.1 0.0 4.8e-58 4.8e-58 1 183 [] 2 189 .. 2 189 .. 0.97 Alignments for each domain: == domain 1 score: 182.1 bits; conditional E-value: 4.8e-58 TIGR00070 1 lriAlpKGrleeetlkllekaglklskkeerkliasaedeev.evlllrakdiptyvekgaadlGitGk 68 l + lpKG+le+ t++l+++a+l+++++++r++ as++d+++ +v +lr+++ipty+e+g +dlGitG lcl|NCBI__GCF_000024385.1:WP_012853319.1 2 LSLVLPKGSLEKATMELFDAADLTVRRSSDRDYRASIDDPRIdRVRVLRPQEIPTYIEQGLFDLGITGR 70 6789*************************************978999********************** PP TIGR00070 69 DlleEseadvvelldlgfgkc.....klvlAvpeesdvesledlkegkriATkypnltreylekkgvkv 132 D+++E ++dvv l +l+++k+ ++v+Avp++ ++++++dl eg ri T++p+lt+++lek+gvk+ lcl|NCBI__GCF_000024385.1:WP_012853319.1 71 DWITETDSDVVSLGQLQYSKAtsnpvRVVMAVPKDAPWQKVSDLPEGVRISTEFPSLTQRFLEKHGVKA 139 ********************9999999****************************************** PP TIGR00070 133 eivkleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183 ++v+++Ga+E+++ ++ daIvD++etG++Lr+ngL+i++++l+s + l+a lcl|NCBI__GCF_000024385.1:WP_012853319.1 140 TVVPSYGATEAKV-PDIVDAIVDLTETGSSLRKNGLRILDTLLTSYTELVA 189 **********665.9********************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (291 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: 8.84 // [ok]
This GapMind analysis is from Apr 10 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