Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_013430203.1 CALKRO_RS06250 ATP phosphoribosyltransferase
Query= reanno::WCS417:GFF870 (211 letters) >NCBI__GCF_000166775.1:WP_013430203.1 Length = 209 Score = 181 bits (458), Expect = 1e-50 Identities = 102/210 (48%), Positives = 144/210 (68%), Gaps = 6/210 (2%) Query: 1 MLTIALSKGRILDDTLPLLAEAGIVPTENPDKSRKLIIPTTQDDVRLLIVRATDVPTYVE 60 M+TIAL KGR+ T+ LL A +V + ++SRKLII TQ+ +R L+V+ DVPTYVE Sbjct: 1 MITIALPKGRLAQQTVELLKRASLVDIDISEESRKLIIEDTQNSLRFLMVKPFDVPTYVE 60 Query: 61 HGAADLGVAGKDVLMEYGGQGLYEPLDLRIALCKLMTAGRVGDVE---PKGRLRVATKFV 117 +G AD+GV GKDVL+E + +YE LDL+I C + AG G E K +ATKF Sbjct: 61 YGVADVGVVGKDVLLEM-NKRVYELLDLKIGKCFVALAGPKGISEALLKKPDKTIATKFP 119 Query: 118 NVAKRYYAE-QGRQVDIIKLYGSMELAPLIGLADKIIDVVDTGNTLRANGLEPQEFIADI 176 N+AK Y+ +G V IIKL GS+ELAP++GL+D I+D+V++G TL+ NGLE E + DI Sbjct: 120 NIAKEYFENVRGEDVKIIKLNGSVELAPILGLSDMIVDIVESGRTLKENGLEVYEKLYDI 179 Query: 177 SSRLIVNKASMKMQHARIQALIDTLRKAVE 206 S+RLI N+AS+K++ +I +I+ L + +E Sbjct: 180 SARLIANRASLKLK-TQIDDIINRLERMIE 208 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: 160 Number of extensions: 4 Number of successful extensions: 4 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: 209 Length adjustment: 21 Effective length of query: 190 Effective length of database: 188 Effective search space: 35720 Effective search space used: 35720 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_013430203.1 CALKRO_RS06250 (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.2178506.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-66 207.9 0.1 6.8e-66 207.7 0.1 1.0 1 NCBI__GCF_000166775.1:WP_013430203.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013430203.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 207.7 0.1 6.8e-66 6.8e-66 1 183 [] 2 185 .. 2 185 .. 0.94 Alignments for each domain: == domain 1 score: 207.7 bits; conditional E-value: 6.8e-66 TIGR00070 1 lriAlpKGrleeetlklleka...glklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDl 70 ++iAlpKGrl+++t++ll++a ++++s+++ rkli++++++ +++l++++ d+ptyve+g+ad+G++GkD+ NCBI__GCF_000166775.1:WP_013430203.1 2 ITIALPKGRLAQQTVELLKRAslvDIDISEES-RKLIIEDTQNSLRFLMVKPFDVPTYVEYGVADVGVVGKDV 73 79*******************87788888888.**************************************** PP TIGR00070 71 leEseadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkg.vkveivkleGavE 142 l E ++ v+elldl++gkc ++lA p+ + l+ k++k iATk+pn+++ey+e+ + +v+i+kl+G+vE NCBI__GCF_000166775.1:WP_013430203.1 74 LLEMNKRVYELLDLKIGKCFVALAGPKGISEALLK--KPDKTIATKFPNIAKEYFENVRgEDVKIIKLNGSVE 144 ****************************9444422..3379***************97769************ PP TIGR00070 143 lapllgladaIvDivetGttLrengLkiieeilessarlia 183 lap+lgl+d+IvDive+G+tL+engL+++e+++++sarlia NCBI__GCF_000166775.1:WP_013430203.1 145 LAPILGLSDMIVDIVESGRTLKENGLEVYEKLYDISARLIA 185 ***************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (209 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: 11.12 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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