Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate CA265_RS03640 CA265_RS03640 ATP phosphoribosyltransferase
Query= BRENDA::Q5HSJ4 (299 letters) >FitnessBrowser__Pedo557:CA265_RS03640 Length = 283 Score = 233 bits (594), Expect = 4e-66 Identities = 123/293 (41%), Positives = 189/293 (64%), Gaps = 13/293 (4%) Query: 7 LRIAIQKSGRLSKESIELLSECGVKMHIHEQSLIAFSTNLPIDILRVRDDDIPGLIFDGV 66 L+IAIQKSGRL+++S+E+L CG+ ++ SLI+ TN P++IL +RDDDIP + DG+ Sbjct: 4 LKIAIQKSGRLNEKSVEILKNCGLSFENYKSSLISTVTNFPLEILFLRDDDIPEYVQDGI 63 Query: 67 VDLGIIGENVLEENELERQSLGENPSYKLLKKLDFGYCRLSLALPQENKFQNLKDFEGLR 126 DLGI+GENV+ E + E L+KL FG C L +A+ + Q L++ G Sbjct: 64 ADLGIVGENVIVETKAE---------VDYLQKLGFGKCTLKIAVQATSNIQKLEELNGKA 114 Query: 127 IATSYPQLLKRFMKENGINYKNCTLTGSVEVAPRANLADAICDLVSSGATLQANNLKEVK 186 IATSYP +L++F++E GI T++GSVE+ P L+DAI D+VS+G TL++N LK Sbjct: 115 IATSYPVILEKFLQEKGIKSDIRTISGSVEIGPGLGLSDAIFDIVSTGGTLKSNGLKPFA 174 Query: 187 VIYESRACLIQKENALSKEKQALVDKIMLRVAGVMQARESKYIMLHAPKEKLDKIQALLP 246 + +S A LI ++ + V +++ R+ V+ A+ +KY++L+ K+ L K+ LLP Sbjct: 175 DVMQSEAVLIGNKSIADNPE---VAELLQRIRSVLSAKSNKYVVLNVSKDNLQKVVDLLP 231 Query: 247 GVERPTILPLAHDEKNVALHMVSKENLFWETMEALKEEGASSILVLPIEKMLK 299 GV+ PT++PL + VA+H V E FW+ + +LK GA ILV+PIEK+++ Sbjct: 232 GVKSPTVVPL-FEPNWVAVHSVIAEEDFWDKINSLKAAGAEGILVMPIEKIIR 283 Lambda K H 0.317 0.135 0.371 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: 233 Number of extensions: 12 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: 299 Length of database: 283 Length adjustment: 26 Effective length of query: 273 Effective length of database: 257 Effective search space: 70161 Effective search space used: 70161 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 (21.6 bits) S2: 48 (23.1 bits)
Align candidate CA265_RS03640 CA265_RS03640 (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.25939.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-60 190.5 0.1 2.1e-60 189.8 0.1 1.3 1 lcl|FitnessBrowser__Pedo557:CA265_RS03640 CA265_RS03640 ATP phosphoribosyl Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS03640 CA265_RS03640 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 189.8 0.1 2.1e-60 2.1e-60 1 182 [. 4 184 .. 4 185 .. 0.99 Alignments for each domain: == domain 1 score: 189.8 bits; conditional E-value: 2.1e-60 TIGR00070 1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitG 67 l+iA++ Grl e+++++l+++gl++++ + +li ++++ ++e+l+lr++dip+yv++g+adlGi+G lcl|FitnessBrowser__Pedo557:CA265_RS03640 4 LKIAIQkSGRLNEKSVEILKNCGLSFENYK-SSLISTVTNFPLEILFLRDDDIPEYVQDGIADLGIVG 70 89****99********************99.99*********************************** PP TIGR00070 68 kDlleEseadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveiv 135 ++++ E +a+v l +lgfgkc+l +Av+ +s++++le+l+ gk iAT+yp + +++l++kg+k +i lcl|FitnessBrowser__Pedo557:CA265_RS03640 71 ENVIVETKAEVDYLQKLGFGKCTLKIAVQATSNIQKLEELN-GKAIATSYPVILEKFLQEKGIKSDIR 137 *****************************************.9************************* PP TIGR00070 136 kleGavElapllgladaIvDivetGttLrengLkiieeilessarli 182 ++G+vE+ p lgl+daI+Div+tG tL++ngLk ++++++s+a+li lcl|FitnessBrowser__Pedo557:CA265_RS03640 138 TISGSVEIGPGLGLSDAIFDIVSTGGTLKSNGLKPFADVMQSEAVLI 184 **********************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (283 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: 12.13 // [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