Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_012284034.1 HM1_RS13885 ATP phosphoribosyltransferase
Query= reanno::WCS417:GFF870 (211 letters) >NCBI__GCF_000019165.1:WP_012284034.1 Length = 219 Score = 180 bits (457), Expect = 2e-50 Identities = 95/215 (44%), Positives = 141/215 (65%), Gaps = 10/215 (4%) Query: 1 MLTIALSKGRILDDTLPLLAEAGIVPTENPDKSRKLIIPTTQDDVRLLIVRATDVPTYVE 60 MLT+AL KG++ DD + LL EAG+ + SRKL+I +D V+ +I R TD+PT+VE Sbjct: 4 MLTVALPKGKLFDDAVELLREAGLNTKGLSENSRKLVIHQEKDRVKYIICRPTDIPTFVE 63 Query: 61 HGAADLGVAGKDVLMEYGGQGLYEPLDLRIALCKLMTAGRVGDVEPKGR-------LRVA 113 +GAAD G+ GKD ++E + + E +DLR C+ + A + D KGR RVA Sbjct: 64 YGAADFGIVGKDTIVEQD-KDIMELVDLRFGFCRFVVA--LPDAAAKGRDLTQFNYRRVA 120 Query: 114 TKFVNVAKRYYAEQGRQVDIIKLYGSMELAPLIGLADKIIDVVDTGNTLRANGLEPQEFI 173 TKF VA+ ++AE+G QV+IIKL+G++ELAP +GLAD I+D+V TG TL+ N L E I Sbjct: 121 TKFPKVAESFFAEKGMQVEIIKLHGNIELAPAVGLADMIVDIVSTGRTLKENNLTAVEEI 180 Query: 174 ADISSRLIVNKASMKMQHARIQALIDTLRKAVESR 208 ++RL+ N+ S +++H RIQ ++ +R V+ + Sbjct: 181 FTATARLVANRVSYRLKHKRIQPFVERVRSLVKDK 215 Lambda K H 0.320 0.138 0.384 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: 143 Number of extensions: 3 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: 211 Length of database: 219 Length adjustment: 22 Effective length of query: 189 Effective length of database: 197 Effective search space: 37233 Effective search space used: 37233 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 45 (21.9 bits)
Align candidate WP_012284034.1 HM1_RS13885 (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.17355.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-69 218.3 0.1 4.3e-69 218.1 0.1 1.0 1 lcl|NCBI__GCF_000019165.1:WP_012284034.1 HM1_RS13885 ATP phosphoribosyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019165.1:WP_012284034.1 HM1_RS13885 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 218.1 0.1 4.3e-69 4.3e-69 1 183 [] 5 189 .. 5 189 .. 0.97 Alignments for each domain: == domain 1 score: 218.1 bits; conditional E-value: 4.3e-69 TIGR00070 1 lriAlpKGrleeetlkllekaglklskke..erkliasaedeevevlllrakdiptyvekgaadlGitG 67 l++AlpKG+l++++++ll++agl+ + + +rkl++++e+++v+++++r++dipt+ve+gaad+Gi+G lcl|NCBI__GCF_000019165.1:WP_012284034.1 5 LTVALPKGKLFDDAVELLREAGLNTKGLSenSRKLVIHQEKDRVKYIICRPTDIPTFVEYGAADFGIVG 73 79**********************88766669************************************* PP TIGR00070 68 kDlleEseadvvelldlgfgkcklvlAvpees.dvesledlkegkriATkypnltreylekkgvkveiv 135 kD++ E+++d++el+dl+fg c++v+A p++ + ++l++++ +r+ATk+p+++++++++kg++vei+ lcl|NCBI__GCF_000019165.1:WP_012284034.1 74 KDTIVEQDKDIMELVDLRFGFCRFVVALPDAAaKGRDLTQFN-YRRVATKFPKVAESFFAEKGMQVEII 141 *******************************97888888888.79************************ PP TIGR00070 136 kleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183 kl+G++Elap++glad+IvDiv+tG+tL+en+L +eei++++arl+a lcl|NCBI__GCF_000019165.1:WP_012284034.1 142 KLHGNIELAPAVGLADMIVDIVSTGRTLKENNLTAVEEIFTATARLVA 189 **********************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (219 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: 6.92 // [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