Align ATP phosphoribosyltransferase (characterized)
to candidate WP_085217032.1 B9N75_RS00535 ATP phosphoribosyltransferase
Query= CharProtDB::CH_024688 (299 letters) >NCBI__GCF_900177405.1:WP_085217032.1 Length = 296 Score = 291 bits (744), Expect = 2e-83 Identities = 154/297 (51%), Positives = 202/297 (68%), Gaps = 4/297 (1%) Query: 2 TDNTRLRIAMQKSGRLSDDSRELLARCGIKINLHTQRLIAMAENMPIDILRVRDDDIPGL 61 TD++RL IA+QKSGRL++ SR LL G+++ L A EN P D++ VRDDDIP Sbjct: 3 TDDSRLHIAIQKSGRLAEQSRRLLRDAGLRLQEGKNALTARIENFPADLMYVRDDDIPTF 62 Query: 62 VMDGVVDLGIIGENVLEEELLNRRAQGEDPRYFTLRRLDFGGCRLSLATPVDEAWDGPLS 121 V DGV +LGI+G NVL E L R D RY L L FG C L LA W G Sbjct: 63 VADGVCELGIVGSNVLREFELAER----DSRYEILSPLGFGRCALKLAAAATSDWHGLAD 118 Query: 122 LNGKRIATSYPHLLKRYLDQKGISFKSCLLNGSVEVAPRAGLADAICDLVSTGATLEANG 181 L RIATSYPH+++ +L+Q+ I+ +NG+VE+APR G+A ICDLVSTGATLEANG Sbjct: 119 LGEARIATSYPHIVRDFLEQRQIAATVVTMNGAVELAPRLGIAPFICDLVSTGATLEANG 178 Query: 182 LREVEVIYRSKACLIQRDGEMEESKQQLIDKLLTRIQGVIQARESKYIMMHAPTERLDEV 241 LR +E ++ S+A L++ G ++E++Q+ ++ L+ RI GV+ +ESKYIM++AP L + Sbjct: 179 LRPLETLFESEAVLVRTRGALDEARQETMNGLVRRIGGVLATKESKYIMLNAPEAALPAI 238 Query: 242 IALLPGAERPTILPLAGDQQRVAMHMVSSETLFWETMEKLKALGASSILVLPIEKMM 298 ALLPGAE PTILPL + A+H V E++FWET+ KLKA GAS+ILVLPIEKMM Sbjct: 239 SALLPGAEAPTILPLHARPGQFAVHAVCQESVFWETLHKLKANGASAILVLPIEKMM 295 Lambda K H 0.320 0.137 0.389 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: 272 Number of extensions: 9 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: 299 Length of database: 296 Length adjustment: 26 Effective length of query: 273 Effective length of database: 270 Effective search space: 73710 Effective search space used: 73710 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: 48 (23.1 bits)
Align candidate WP_085217032.1 B9N75_RS00535 (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.69534.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-57 180.5 0.0 1.9e-57 180.1 0.0 1.1 1 NCBI__GCF_900177405.1:WP_085217032.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900177405.1:WP_085217032.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 180.1 0.0 1.9e-57 1.9e-57 1 182 [. 8 193 .. 8 194 .. 0.96 Alignments for each domain: == domain 1 score: 180.1 bits; conditional E-value: 1.9e-57 TIGR00070 1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDlle 72 l+iA++ Grl+e++ +ll++agl+l++ + +l+a++e+ + +++++r++dipt+v++g+ +lGi+G+++l+ NCBI__GCF_900177405.1:WP_085217032.1 8 LHIAIQkSGRLAEQSRRLLRDAGLRLQEGK-NALTARIENFPADLMYVRDDDIPTFVADGVCELGIVGSNVLR 79 78****99*******************999.9***************************************** PP TIGR00070 73 E.....seadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkleGa 140 E +++ ++ l lgfg+c l lA+ +sd++ l+dl ++riAT+yp+++r++le++++ +++v ++Ga NCBI__GCF_900177405.1:WP_085217032.1 80 EfelaeRDSRYEILSPLGFGRCALKLAAAATSDWHGLADLG-EARIATSYPHIVRDFLEQRQIAATVVTMNGA 151 *87754455599999**************************.79***************************** PP TIGR00070 141 vElapllgladaIvDivetGttLrengLkiieeilessarli 182 vElap+lg+a +I+D+v+tG+tL++ngL+ +e+++es+a+l+ NCBI__GCF_900177405.1:WP_085217032.1 152 VELAPRLGIAPFICDLVSTGATLEANGLRPLETLFESEAVLV 193 ****************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (296 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: 13.97 // [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