Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate N515DRAFT_2938 N515DRAFT_2938 ATP phosphoribosyltransferase
Query= BRENDA::Q5HSJ4 (299 letters) >FitnessBrowser__Dyella79:N515DRAFT_2938 Length = 297 Score = 244 bits (622), Expect = 2e-69 Identities = 129/299 (43%), Positives = 184/299 (61%), Gaps = 4/299 (1%) Query: 1 MQENTRLRIAIQKSGRLSKESIELLSECGVKMHIHEQSLIAFSTNLPIDILRVRDDDIPG 60 M+ RLRIA+QKSGRL++ +++LL+ CG+ L F P+D+L VRDDDIPG Sbjct: 1 MKPRDRLRIAMQKSGRLTEPALDLLNRCGLTFRQSRDKLFLFGEGEPVDLLLVRDDDIPG 60 Query: 61 LIFDGVVDLGIIGENVLEENEL-ERQSLGENPSYKLLKKLDFGYCRLSLALPQENKFQNL 119 LI GV DLGI+G NVL E + + G ++ L FG CRLS+A+PQE ++ Sbjct: 61 LIAQGVCDLGIVGRNVLSEYSFTDGREAGPLAEWR---SLGFGRCRLSIAVPQEMNYEQP 117 Query: 120 KDFEGLRIATSYPQLLKRFMKENGINYKNCTLTGSVEVAPRANLADAICDLVSSGATLQA 179 + GLRIATSYP LL+ +++ G++ TL GSVE+APR AD ICDLV SG TL A Sbjct: 118 QQLAGLRIATSYPGLLRDWLRNQGVDAGVVTLAGSVEIAPRLGTADLICDLVQSGGTLVA 177 Query: 180 NNLKEVKVIYESRACLIQKENALSKEKQALVDKIMLRVAGVMQARESKYIMLHAPKEKLD 239 N L+E V+ ES A L + E+ +++ ++ R+ GVMQ RES+ ++L ++ LD Sbjct: 178 NQLREADVLLESEAVLAGPRTLPTDERGDMIELLLKRLDGVMQVRESRLLLLQTSRQHLD 237 Query: 240 KIQALLPGVERPTILPLAHDEKNVALHMVSKENLFWETMEALKEEGASSILVLPIEKML 298 + LLPG +PT+LP+A + L + + W +E +K+ GA + VLP+EKML Sbjct: 238 AVTRLLPGGPQPTLLPVAGQPDQLMLQALCAGEVSWRQLEEIKKAGAREMFVLPVEKML 296 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: 246 Number of extensions: 12 Number of successful extensions: 2 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: 297 Length adjustment: 27 Effective length of query: 272 Effective length of database: 270 Effective search space: 73440 Effective search space used: 73440 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 N515DRAFT_2938 N515DRAFT_2938 (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.31011.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-57 179.3 0.0 4.7e-57 178.9 0.0 1.2 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_2938 N515DRAFT_2938 ATP phosphoribosy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_2938 N515DRAFT_2938 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 178.9 0.0 4.7e-57 4.7e-57 1 181 [. 7 193 .. 7 195 .. 0.96 Alignments for each domain: == domain 1 score: 178.9 bits; conditional E-value: 4.7e-57 TIGR00070 1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGi 65 lriA++ Grl e++l+ll+++gl++++++ +kl+ e e+v++ll+r++dip +++g+ dlGi lcl|FitnessBrowser__Dyella79:N515DRAFT_2938 7 LRIAMQkSGRLTEPALDLLNRCGLTFRQSR-DKLFLFGEGEPVDLLLVRDDDIPGLIAQGVCDLGI 71 89****99**********************.99********************************* PP TIGR00070 66 tGkDlleE....sead.....vvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltr 122 +G ++l E + ++e+ +lgfg+c+l++Avp+e ++e++++l+ g riAT+yp l r lcl|FitnessBrowser__Dyella79:N515DRAFT_2938 72 VGRNVLSEysftD--GreagpLAEWRSLGFGRCRLSIAVPQEMNYEQPQQLA-GLRIATSYPGLLR 134 ********76552..045778*******************************.9************ PP TIGR00070 123 eylekkgvkveivkleGavElapllgladaIvDivetGttLrengLkiieeilessarl 181 ++l+++gv++ +v l G+vE+ap+lg+ad+I+D+v++G tL +n+L++ +++les+a+l lcl|FitnessBrowser__Dyella79:N515DRAFT_2938 135 DWLRNQGVDAGVVTLAGSVEIAPRLGTADLICDLVQSGGTLVANQLREADVLLESEAVL 193 *********************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (297 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: 7.39 // [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