Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_106709262.1 CU102_RS01965 ATP phosphoribosyltransferase
Query= reanno::Smeli:SMc00917 (231 letters) >NCBI__GCF_003010955.1:WP_106709262.1 Length = 231 Score = 309 bits (791), Expect = 3e-89 Identities = 152/210 (72%), Positives = 177/210 (84%) Query: 1 MTVTIALPSKGRMKDEASAIFERAGMKIAAVGSDRSYRGRVEGWDDVEIAYLSASEIARE 60 MT+T+ALPSKGR+K+EA + + AG+ + R+YR +V+G ++I +LSASEIARE Sbjct: 1 MTITLALPSKGRLKEEALGVLKNAGLSVILPKDQRNYRAQVKGESQIDILFLSASEIARE 60 Query: 61 IGSGAVDFGVTGEDLVREGLADADARVDFAARLGFGHADVVVAVPEIWYDVDTMADLGDV 120 +G G+VD GVTGEDL+RE L+ AD RV A+LGFGHADVVVAVPE+WYDV TMADL DV Sbjct: 61 LGYGSVDLGVTGEDLIRETLSSADERVQIEAQLGFGHADVVVAVPEVWYDVSTMADLDDV 120 Query: 121 AADFRARHGRRLAIATKYWRLTQQFFSGSHGIQLYRIVESLGATEGAPASGSADIIVDIT 180 AADFR RHGRRL IATKYWRLTQQFFS HGIQ+YRIVESLGATEGAPASGSADIIVDIT Sbjct: 121 AADFRQRHGRRLRIATKYWRLTQQFFSQMHGIQVYRIVESLGATEGAPASGSADIIVDIT 180 Query: 181 STGSTLKANHLKILSDGVILRSEACLVRAR 210 STGSTL ANHLK+L DGVIL+S+ACLV +R Sbjct: 181 STGSTLHANHLKVLDDGVILKSQACLVSSR 210 Lambda K H 0.320 0.135 0.386 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: 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: 231 Length of database: 231 Length adjustment: 23 Effective length of query: 208 Effective length of database: 208 Effective search space: 43264 Effective search space used: 43264 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 (21.8 bits) S2: 46 (22.3 bits)
Align candidate WP_106709262.1 CU102_RS01965 (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.2102153.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-58 181.6 0.1 8.4e-58 181.3 0.1 1.0 1 NCBI__GCF_003010955.1:WP_106709262.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010955.1:WP_106709262.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 181.3 0.1 8.4e-58 8.4e-58 1 182 [. 3 207 .. 3 208 .. 0.93 Alignments for each domain: == domain 1 score: 181.3 bits; conditional E-value: 8.4e-58 TIGR00070 1 lriAlp.KGrleeetlkllekaglklskke.erkliasaede.evevlllrakdiptyvekgaadlGitGkDl 70 +++Alp KGrl+ee+l +l++agl++ ++ +r++ a+++ e ++++l+l+a++i++++ +g++dlG+tG+Dl NCBI__GCF_003010955.1:WP_106709262.1 3 ITLALPsKGRLKEEALGVLKNAGLSVILPKdQRNYRAQVKGEsQIDILFLSASEIARELGYGSVDLGVTGEDL 75 79***********************9988889*****9998736***************************** PP TIGR00070 71 leE....sead..vvelldlgfgkcklvlAvpees.dvesledlke.........gk..riATkypnltreyl 125 ++E d v+ ++lgfg++++v+Avpe + dv++++dl++ g+ riATky +lt++++ NCBI__GCF_003010955.1:WP_106709262.1 76 IREtlssA--DerVQIEAQLGFGHADVVVAVPEVWyDVSTMADLDDvaadfrqrhGRrlRIATKYWRLTQQFF 146 ***77433..35599999**********************************9983358************** PP TIGR00070 126 ekkg.vk.veivkleGavElapllgladaIvDivetGttLrengLkiie..eilessarli 182 ++++ ++ ++iv++ Ga+E ap+ g ad+IvDi++tG+tL++n+Lk+++ +il+s+a+l+ NCBI__GCF_003010955.1:WP_106709262.1 147 SQMHgIQvYRIVESLGATEGAPASGSADIIVDITSTGSTLHANHLKVLDdgVILKSQACLV 207 *99887758***************************************9667********8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (231 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: 16.99 // [ok]
This GapMind analysis is from Jul 26 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