Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_066326080.1 BLR17_RS14025 ATP phosphoribosyltransferase
Query= BRENDA::Q5HSJ4 (299 letters) >NCBI__GCF_900100165.1:WP_066326080.1 Length = 285 Score = 233 bits (595), Expect = 3e-66 Identities = 121/292 (41%), Positives = 198/292 (67%), Gaps = 11/292 (3%) Query: 7 LRIAIQKSGRLSKESIELLSECGVKMHIHEQSLIAFSTNLPIDILRVRDDDIPGLIFDGV 66 L+IAIQKSGRL+++SI++L + G+ ++ L A ++N P+++L +R+ DIP + DGV Sbjct: 4 LKIAIQKSGRLNEDSIQILKDAGISINNGIDQLKAEASNFPLEVLYLRNSDIPQYLIDGV 63 Query: 67 VDLGIIGENVLEENELERQSLGENPSYKLLKKLDFGYCRLSLALPQENKFQNLKDFEGLR 126 VD+ I+G+N+L E + ++++KL F C++S+A+P+ +++++KD +GLR Sbjct: 64 VDIAIVGDNLLVE---------KGKDIEVIQKLGFSKCKVSVAVPKTFEYKSVKDLDGLR 114 Query: 127 IATSYPQLLKRFMKENGINYKNCTLTGSVEVAPRANLADAICDLVSSGATLQANNLKEVK 186 IATSYP + F + G++ ++GSVE+AP LADAI D+VSSG+TL NNLKEV+ Sbjct: 115 IATSYPNTVIEFFNKFGLSVDIHQISGSVEIAPNIGLADAIVDIVSSGSTLFKNNLKEVE 174 Query: 187 VIYESRACLIQKENALSKEKQALVDKIMLRVAGVMQARESKYIMLHAPKEKLDKIQALLP 246 VI +S A L ++ E Q ++D + R+ V++AR+SKYI+++ P +K+D I +LP Sbjct: 175 VILKSEAVLAVSPK-VTPEAQKIIDTLKFRIESVLRARKSKYILMNVPNDKIDAIGKILP 233 Query: 247 GVERPTILPLAHDEKNVALHMVSKENLFWETMEALKEEGASSILVLPIEKML 298 ++ T++PLA + + ++H V ++ FWE ++ LKE GA ILV PIEKM+ Sbjct: 234 VLKSLTVMPLAQEGWS-SVHSVIDKDTFWEVIDQLKEAGAEGILVCPIEKMV 284 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: 225 Number of extensions: 10 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: 285 Length adjustment: 26 Effective length of query: 273 Effective length of database: 259 Effective search space: 70707 Effective search space used: 70707 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 WP_066326080.1 BLR17_RS14025 (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.2182203.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-60 190.1 0.1 2.2e-60 189.7 0.1 1.1 1 NCBI__GCF_900100165.1:WP_066326080.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066326080.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 189.7 0.1 2.2e-60 2.2e-60 1 182 [. 4 184 .. 4 185 .. 0.99 Alignments for each domain: == domain 1 score: 189.7 bits; conditional E-value: 2.2e-60 TIGR00070 1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDlle 72 l+iA++ Grl e+++++l++ag+++++ ++l a+a++ ++evl+lr++dip+y+ +g++d+ i+G +ll NCBI__GCF_900100165.1:WP_066326080.1 4 LKIAIQkSGRLNEDSIQILKDAGISINNGI-DQLKAEASNFPLEVLYLRNSDIPQYLIDGVVDIAIVGDNLLV 75 89****99**********************.****************************************** PP TIGR00070 73 EseadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkleGavElap 145 E+++d++ + +lgf+kck+++Avp++ +++s++dl+ g riAT+ypn++ e+++k g++v+i +++G+vE+ap NCBI__GCF_900100165.1:WP_066326080.1 76 EKGKDIEVIQKLGFSKCKVSVAVPKTFEYKSVKDLD-GLRIATSYPNTVIEFFNKFGLSVDIHQISGSVEIAP 147 ************************************.9*********************************** PP TIGR00070 146 llgladaIvDivetGttLrengLkiieeilessarli 182 +gladaIvDiv++G+tL +n+Lk++e+il+s+a+l NCBI__GCF_900100165.1:WP_066326080.1 148 NIGLADAIVDIVSSGSTLFKNNLKEVEVILKSEAVLA 184 **********************************995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (285 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: 18.80 // [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