Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_078429924.1 BK574_RS20690 ATP phosphoribosyltransferase
Query= reanno::pseudo5_N2C3_1:AO356_06970 (211 letters) >NCBI__GCF_002019605.1:WP_078429924.1 Length = 213 Score = 181 bits (458), Expect = 1e-50 Identities = 98/207 (47%), Positives = 140/207 (67%), Gaps = 4/207 (1%) Query: 2 LTIALSKGRILDDTLPLLAEAGIVPTENPDKSRKLIIPTTQADVRLLIVRATDVPTYVEH 61 LT+A+ KGRI ++ LL +AG + D SRKLI+ A +R ++ + DVPTYVE+ Sbjct: 5 LTVAMPKGRIFEEAADLLRKAGYALPDEFDDSRKLIVDAPIAKMRFILAKPMDVPTYVEY 64 Query: 62 GAADLGVAGKDVLMEYGGQGLYEPLDLRIARCKLMTAGKVGAPEPKGRL--RVATKFVNI 119 G AD+GVAGKD ++E + +YE LDL+I+ C L AG + E + + +VA+K+ + Sbjct: 65 GVADVGVAGKDTMLEEE-RDVYEVLDLKISECYLAVAG-LPTYEKQSEIAPKVASKYPQV 122 Query: 120 AKRYYAEQGRQVDIIKLYGSMELAPLIGLADKIIDVVDTGNTLRANGLEPQDFIADITSR 179 A +Y+ EQG QV++IKL GS+ELAPL+GLAD+I+D+V TG TL+ NGL + I DITSR Sbjct: 123 AIQYFKEQGEQVEVIKLNGSIELAPLVGLADRIVDIVSTGRTLKENGLVELEKIMDITSR 182 Query: 180 LIVNKASMKMQHARIQALIDTLRKAVE 206 LIVN S +M+ I L++ L K +E Sbjct: 183 LIVNPVSYRMKDEVIDDLVERLAKVIE 209 Lambda K H 0.320 0.138 0.385 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: 168 Number of extensions: 5 Number of successful extensions: 3 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: 213 Length adjustment: 21 Effective length of query: 190 Effective length of database: 192 Effective search space: 36480 Effective search space used: 36480 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_078429924.1 BK574_RS20690 (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.23678.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-64 201.0 0.1 9e-64 200.8 0.1 1.0 1 lcl|NCBI__GCF_002019605.1:WP_078429924.1 BK574_RS20690 ATP phosphoribosyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078429924.1 BK574_RS20690 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 200.8 0.1 9e-64 9e-64 1 183 [] 5 185 .. 5 185 .. 0.97 Alignments for each domain: == domain 1 score: 200.8 bits; conditional E-value: 9e-64 TIGR00070 1 lriAlpKGrleeetlkllekaglklskke..erkliasaedeevevlllrakdiptyvekgaadlGitG 67 l++A+pKGr++ee+ +ll+kag+ l ++ +rkli++a+ ++++++l++++d+ptyve+g+ad+G+ G lcl|NCBI__GCF_002019605.1:WP_078429924.1 5 LTVAMPKGRIFEEAADLLRKAGYALPDEFddSRKLIVDAPIAKMRFILAKPMDVPTYVEYGVADVGVAG 73 79**********************9988778************************************** PP TIGR00070 68 kDlleEseadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivk 136 kD++ E+e+dv+e+ldl++++c l++A + + +s ++++ ++A+kyp+++ +y++++g +ve++k lcl|NCBI__GCF_002019605.1:WP_078429924.1 74 KDTMLEEERDVYEVLDLKISECYLAVAGLPTYEKQS--EIAP--KVASKYPQVAIQYFKEQGEQVEVIK 138 ****************************99986666..7875..************************* PP TIGR00070 137 leGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183 l+G++Elapl+glad IvDiv+tG+tL+engL+++e+i+++++rli+ lcl|NCBI__GCF_002019605.1:WP_078429924.1 139 LNGSIELAPLVGLADRIVDIVSTGRTLKENGLVELEKIMDITSRLIV 185 *********************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (213 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: 6.82 // [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