Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate 3609569 Dshi_2953 ATP phosphoribosyltransferase (RefSeq)
Query= reanno::Phaeo:GFF2940 (230 letters) >FitnessBrowser__Dino:3609569 Length = 239 Score = 328 bits (842), Expect = 4e-95 Identities = 164/221 (74%), Positives = 188/221 (85%) Query: 1 MSLKLGVPSKGRLMEKTFEWFAKRGITLSRTGSDREYAGAVAGIDGIDLVLLSAGEMPRE 60 M+LKLGVPSKGRLM+KTF+WF + GITL RTGS+REYAG+V G+DG+ LVLLSAGE+PRE Sbjct: 1 MTLKLGVPSKGRLMDKTFDWFGRHGITLQRTGSEREYAGSVDGVDGVALVLLSAGEIPRE 60 Query: 61 LAAGRIHLGVTGTDLVQEKLPLWEQQVEEIAGLGFGHADLILAVPQIWVDVETIDDLDAV 120 LAAGRIHLGVTGTDLVQEKLP W +QV IA LGFGHADLILAVP+ W+DVET+DDLDAV Sbjct: 61 LAAGRIHLGVTGTDLVQEKLPDWMRQVRSIAPLGFGHADLILAVPKCWIDVETLDDLDAV 120 Query: 121 AAAFRAKHGHRLRIATKYHRLVREYLMDAGVADYQLVDSQGATEGTVKNETAEMVADITS 180 AA FRA HG RLRIATKYHRLV +L GVADYQLVDSQGATEGTV N TAE +ADITS Sbjct: 121 AAQFRANHGFRLRIATKYHRLVHSHLSAHGVADYQLVDSQGATEGTVANLTAEAIADITS 180 Query: 181 TGETLRANHLKLMSDGLILRSQATLWRSRVAKYSAKEKATL 221 TGETLRANHLK++ +L+SQATL+ SR+A + +A + Sbjct: 181 TGETLRANHLKILKGEPVLKSQATLFASRMADWDPTARAAM 221 Lambda K H 0.318 0.134 0.385 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: 260 Number of extensions: 9 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: 230 Length of database: 239 Length adjustment: 23 Effective length of query: 207 Effective length of database: 216 Effective search space: 44712 Effective search space used: 44712 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 3609569 Dshi_2953 (ATP phosphoribosyltransferase (RefSeq))
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.4690.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-54 168.4 0.0 8.9e-54 168.2 0.0 1.0 1 lcl|FitnessBrowser__Dino:3609569 Dshi_2953 ATP phosphoribosyltran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3609569 Dshi_2953 ATP phosphoribosyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 168.2 0.0 8.9e-54 8.9e-54 1 182 [. 3 206 .. 3 207 .. 0.94 Alignments for each domain: == domain 1 score: 168.2 bits; conditional E-value: 8.9e-54 TIGR00070 1 lriAlp.KGrleeetlkllekaglklskke.erkliasaed.eevevlllrakdiptyvekgaadlGitGkDlleE. 73 l++++p KGrl+++t++++ ++g++l+++ er++ s++ ++v ++ll+a +ip++++ g+++lG+tG+Dl++E lcl|FitnessBrowser__Dino:3609569 3 LKLGVPsKGRLMDKTFDWFGRHGITLQRTGsEREYAGSVDGvDGVALVLLSAGEIPRELAAGRIHLGVTGTDLVQEk 79 79***************************999999998887357********************************6 PP TIGR00070 74 ...seadvvelldlgfgkcklvlAvpees.dvesledlke...........gkriATkypnltreylekkg.vkvei 134 + ++v ++ lgfg+++l+lAvp+ + dve+l+dl++ + riATky++l++++l+ +g +++++ lcl|FitnessBrowser__Dino:3609569 80 lpdWMRQVRSIAPLGFGHADLILAVPKCWiDVETLDDLDAvaaqfranhgfRLRIATKYHRLVHSHLSAHGvADYQL 156 6655666***************************************9976445******************889*** PP TIGR00070 135 vkleGavElapllgladaIvDivetGttLrengLkiie..eilessarli 182 v+++Ga+E +++ +a+aI+Di++tG+tLr+n+Lki++ +l+s+a+l+ lcl|FitnessBrowser__Dino:3609569 157 VDSQGATEGTVANLTAEAIADITSTGETLRANHLKILKgePVLKSQATLF 206 *************************************7658*******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (239 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: 6.73 // [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