Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate GFF870 PS417_04415 ATP phosphoribosyltransferase catalytic subunit
Query= reanno::WCS417:GFF870 (211 letters) >FitnessBrowser__WCS417:GFF870 Length = 211 Score = 409 bits (1051), Expect = e-119 Identities = 211/211 (100%), Positives = 211/211 (100%) Query: 1 MLTIALSKGRILDDTLPLLAEAGIVPTENPDKSRKLIIPTTQDDVRLLIVRATDVPTYVE 60 MLTIALSKGRILDDTLPLLAEAGIVPTENPDKSRKLIIPTTQDDVRLLIVRATDVPTYVE Sbjct: 1 MLTIALSKGRILDDTLPLLAEAGIVPTENPDKSRKLIIPTTQDDVRLLIVRATDVPTYVE 60 Query: 61 HGAADLGVAGKDVLMEYGGQGLYEPLDLRIALCKLMTAGRVGDVEPKGRLRVATKFVNVA 120 HGAADLGVAGKDVLMEYGGQGLYEPLDLRIALCKLMTAGRVGDVEPKGRLRVATKFVNVA Sbjct: 61 HGAADLGVAGKDVLMEYGGQGLYEPLDLRIALCKLMTAGRVGDVEPKGRLRVATKFVNVA 120 Query: 121 KRYYAEQGRQVDIIKLYGSMELAPLIGLADKIIDVVDTGNTLRANGLEPQEFIADISSRL 180 KRYYAEQGRQVDIIKLYGSMELAPLIGLADKIIDVVDTGNTLRANGLEPQEFIADISSRL Sbjct: 121 KRYYAEQGRQVDIIKLYGSMELAPLIGLADKIIDVVDTGNTLRANGLEPQEFIADISSRL 180 Query: 181 IVNKASMKMQHARIQALIDTLRKAVESRHRG 211 IVNKASMKMQHARIQALIDTLRKAVESRHRG Sbjct: 181 IVNKASMKMQHARIQALIDTLRKAVESRHRG 211 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: 305 Number of extensions: 5 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: 211 Length of database: 211 Length adjustment: 21 Effective length of query: 190 Effective length of database: 190 Effective search space: 36100 Effective search space used: 36100 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 GFF870 PS417_04415 (ATP phosphoribosyltransferase catalytic subunit)
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.677.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-57 180.4 0.0 2e-57 180.1 0.0 1.1 1 lcl|FitnessBrowser__WCS417:GFF870 PS417_04415 ATP phosphoribosyltr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF870 PS417_04415 ATP phosphoribosyltransferase catalytic subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 180.1 0.0 2e-57 2e-57 1 183 [] 2 182 .. 2 182 .. 0.94 Alignments for each domain: == domain 1 score: 180.1 bits; conditional E-value: 2e-57 TIGR00070 1 lriAlpKGrleeetlkllekaglklskke..erkliasaedeevevlllrakdiptyvekgaadlGitGkDlleEs 74 l+iAl KGr++++tl ll++ag+ +++ +rkli+ +++++v++l++ra+d+ptyve+gaadlG+ GkD+l+E lcl|FitnessBrowser__WCS417:GFF870 2 LTIALSKGRILDDTLPLLAEAGIVPTENPdkSRKLIIPTTQDDVRLLIVRATDVPTYVEHGAADLGVAGKDVLMEY 77 79********************9987766699*******************************************6 PP TIGR00070 75 ead.vvelldlgfgkcklvlAvpeesdvesledlkegk.riATkypnltreylekkgvkveivkleGavElapllg 148 + + ++e ldl++ ckl+ A + ve k g+ r+ATk++n++++y++++g +v+i+kl+G++Elapl+g lcl|FitnessBrowser__WCS417:GFF870 78 GGQgLYEPLDLRIALCKLMTAGRVGD-VEP----K-GRlRVATKFVNVAKRYYAEQGRQVDIIKLYGSMELAPLIG 147 5555*****************99887.444....3.556************************************* PP TIGR00070 149 ladaIvDivetGttLrengLkiieeilessarlia 183 lad I+D+v tG+tLr+ngL+ e i ++s+rli+ lcl|FitnessBrowser__WCS417:GFF870 148 LADKIIDVVDTGNTLRANGLEPQEFIADISSRLIV 182 *********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (211 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: 7.58 // [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