Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate Echvi_2460 Echvi_2460 ATP phosphoribosyltransferase
Query= BRENDA::Q5HSJ4 (299 letters) >FitnessBrowser__Cola:Echvi_2460 Length = 286 Score = 270 bits (690), Expect = 3e-77 Identities = 142/292 (48%), Positives = 198/292 (67%), Gaps = 11/292 (3%) Query: 7 LRIAIQKSGRLSKESIELLSECGVKMHIHEQSLIAFSTNLPIDILRVRDDDIPGLIFDGV 66 +RIA+QKSGRLS++S+ L+ ECG+K + L + STN PI+ L +RDDDIPG + DGV Sbjct: 5 IRIAVQKSGRLSEDSLSLIKECGIKFYNGTGKLKSTSTNFPIEFLYLRDDDIPGYVADGV 64 Query: 67 VDLGIIGENVLEENELERQSLGENPSYKLLKKLDFGYCRLSLALPQENKFQNLKDFEGLR 126 DLGI+GEN L E + S +LKKL F CRLSLA+P+ ++ L FEG Sbjct: 65 ADLGIVGENELVEKD---------KSVDVLKKLGFSKCRLSLAIPKSQEYPGLSYFEGKN 115 Query: 127 IATSYPQLLKRFMKENGINYKNCTLTGSVEVAPRANLADAICDLVSSGATLQANNLKEVK 186 IATSY ++L ++K N IN + ++GSVE+AP LA+ ICD+VSSG+TL N LKEV+ Sbjct: 116 IATSYTKILGDYLKANHINAEIHEISGSVEIAPSIGLAEGICDIVSSGSTLMMNGLKEVE 175 Query: 187 VIYESRACLIQKENALSKEKQALVDKIMLRVAGVMQARESKYIMLHAPKEKLDKIQALLP 246 I++S A LI L+ EK A+V+K++ R+ V + +KY++L+AP E LDKI +L+P Sbjct: 176 EIFKSEAVLI-SHKGLNSEKMAIVEKLLFRINAVQTGKSNKYVLLNAPNESLDKIISLIP 234 Query: 247 GVERPTILPLAHDEKNVALHMVSKENLFWETMEALKEEGASSILVLPIEKML 298 G+ PTILPLA + + ++H V E+ FWE +E L+ GA ILV+PIEKM+ Sbjct: 235 GMRSPTILPLAQEGWS-SVHSVLSEDQFWENIEELRAAGAEGILVVPIEKMV 285 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: 251 Number of extensions: 13 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: 286 Length adjustment: 26 Effective length of query: 273 Effective length of database: 260 Effective search space: 70980 Effective search space used: 70980 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 Echvi_2460 Echvi_2460 (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.5039.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-58 183.9 0.0 1.8e-58 183.5 0.0 1.1 1 lcl|FitnessBrowser__Cola:Echvi_2460 Echvi_2460 ATP phosphoribosyltra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2460 Echvi_2460 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 183.5 0.0 1.8e-58 1.8e-58 1 182 [. 5 185 .. 5 186 .. 0.98 Alignments for each domain: == domain 1 score: 183.5 bits; conditional E-value: 1.8e-58 TIGR00070 1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDlleE 73 +riA++ Grl+e++l+l++++g+k+ + + kl ++++ ++e+l+lr++dip yv++g+adlGi+G++ l E lcl|FitnessBrowser__Cola:Echvi_2460 5 IRIAVQkSGRLSEDSLSLIKECGIKFYNGT-GKLKSTSTNFPIEFLYLRDDDIPGYVADGVADLGIVGENELVE 77 79****99*******************999.8999999999********************************* PP TIGR00070 74 seadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkleGavElapll 147 ++++v l++lgf+kc+l+lA+p+++++ l+ ++ gk iAT+y+++ +yl+ +++++ei +++G+vE+ap++ lcl|FitnessBrowser__Cola:Echvi_2460 78 KDKSVDVLKKLGFSKCRLSLAIPKSQEYPGLSYFE-GKNIATSYTKILGDYLKANHINAEIHEISGSVEIAPSI 150 ********************************999.9************************************* PP TIGR00070 148 gladaIvDivetGttLrengLkiieeilessarli 182 gla+ I+Div++G+tL ngLk++eei++s+a+li lcl|FitnessBrowser__Cola:Echvi_2460 151 GLAEGICDIVSSGSTLMMNGLKEVEEIFKSEAVLI 185 **********************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (286 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.15 // [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