Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_004511946.1 GMET_RS09595 ATP phosphoribosyltransferase
Query= reanno::Miya:8501229 (293 letters) >NCBI__GCF_000012925.1:WP_004511946.1 Length = 291 Score = 344 bits (882), Expect = 2e-99 Identities = 168/290 (57%), Positives = 219/290 (75%) Query: 4 NNMLKIGIPKGSLEEATVNLFARSGWKIRKHHRNYFPEINDPELTARLCRVQEIPRYLED 63 +N+L +GIPKGSLE ATV LF +SGW+I R+YFP ++D EL +L R QE+ +Y+E Sbjct: 2 SNLLNLGIPKGSLENATVELFRKSGWQISISSRSYFPGVDDDELNCKLIRPQEMGKYVER 61 Query: 64 GVLDVGLTGKDWLLETGADVVTVSDLVYSKVSNRPARWVLAVAGDSPYVRPEDLAGCTIA 123 G +D G+ G+DW+ E +DVV V ++VYSKVS RPARWVL V DS +PEDL G TI+ Sbjct: 62 GTIDAGIAGRDWVRENDSDVVEVCEMVYSKVSRRPARWVLVVTKDSTVQKPEDLHGATIS 121 Query: 124 TELLGVTRRYFEDAGIPVKVQYSWGATEAKVVEGLADAIVEVTETGTTIKAHGLRIIAEV 183 TEL+G T+RYF + IPV V++SWGATEAKVV+GL DAIVEVTETG+TIKA+GLRI+ ++ Sbjct: 122 TELVGFTKRYFAERNIPVNVEFSWGATEAKVVDGLCDAIVEVTETGSTIKANGLRIVCDL 181 Query: 184 LLTNTVLIAGKAAWADPWKRAKIEQIDLLLQGALRADSLVGLKMNVPAHNLDAVLDQLPS 243 + + VLIA KAAWADPWKR KIE I LL+ +L A+ +VGLKMN P ++A+ + LPS Sbjct: 182 MESVPVLIANKAAWADPWKRQKIETIATLLKASLAAEGMVGLKMNAPNDKVEAITEILPS 241 Query: 244 LNSPTVAGLRDSTWYAVEIVVENDLVRDLIPRLRAAGAEGIIEYSLNKVI 293 LN PTV+ L S W ++E V+ VR ++P+L A GA+GIIEYSLNKV+ Sbjct: 242 LNRPTVSHLYKSEWVSIESVLHEKEVRRIVPQLLALGAQGIIEYSLNKVL 291 Lambda K H 0.318 0.136 0.401 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: 308 Number of extensions: 13 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: 293 Length of database: 291 Length adjustment: 26 Effective length of query: 267 Effective length of database: 265 Effective search space: 70755 Effective search space used: 70755 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: 48 (23.1 bits)
Align candidate WP_004511946.1 GMET_RS09595 (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.18241.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-49 152.0 0.0 1.2e-48 151.5 0.0 1.2 1 lcl|NCBI__GCF_000012925.1:WP_004511946.1 GMET_RS09595 ATP phosphoribosylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012925.1:WP_004511946.1 GMET_RS09595 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 151.5 0.0 1.2e-48 1.2e-48 1 183 [] 5 190 .. 5 190 .. 0.97 Alignments for each domain: == domain 1 score: 151.5 bits; conditional E-value: 1.2e-48 TIGR00070 1 lriAlpKGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkD 69 l++++pKG+le+ t++l++k+g+++s ++ r+++ ++d+e+++ l+r++++ +yve+g +d+Gi G D lcl|NCBI__GCF_000012925.1:WP_004511946.1 5 LNLGIPKGSLENATVELFRKSGWQISISS-RSYFPGVDDDELNCKLIRPQEMGKYVERGTIDAGIAGRD 72 789*************************9.*************************************** PP TIGR00070 70 lleEseadvvelldlgfgkc.....klvlAvpeesdvesledlkegkriATkypnltreylekkgvkve 133 +++E+++dvve+ ++ ++k ++vl v+++s+v+++edl+ g+ i T+ + t++y+++++++v+ lcl|NCBI__GCF_000012925.1:WP_004511946.1 73 WVRENDSDVVEVCEMVYSKVsrrpaRWVLVVTKDSTVQKPEDLH-GATISTELVGFTKRYFAERNIPVN 140 ***************9888777777*******************.9*********************** PP TIGR00070 134 ivkleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183 + ++Ga+E++++ gl daIv ++etG+t+++ngL+i+ +++es +lia lcl|NCBI__GCF_000012925.1:WP_004511946.1 141 VEFSWGATEAKVVDGLCDAIVEVTETGSTIKANGLRIVCDLMESVPVLIA 190 ********************************************999986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (291 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: 11.46 // [ok]
This GapMind analysis is from Apr 10 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