Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_012384759.1 BIND_RS08985 ATP phosphoribosyltransferase
Query= reanno::Caulo:CCNA_03626 (320 letters) >NCBI__GCF_000019845.1:WP_012384759.1 Length = 325 Score = 266 bits (681), Expect = 4e-76 Identities = 153/322 (47%), Positives = 197/322 (61%), Gaps = 7/322 (2%) Query: 1 MSTPMIFAIPSKGRLKDQVEAWLADCGFKLEMTGGARGYSAELSGLPGVSVRLLSAGDIA 60 M P++ A+PSKGRL++ V A+ A G L G+R Y L G+ GV V +SA DI Sbjct: 4 MQAPLVLAVPSKGRLQENVAAFFARAGLSLVQGRGSRDYRGTLKGIEGVEVAFVSASDIV 63 Query: 61 AGLDSGDLHLGVTGEDLLRERGDDMDSRVMLLRALGFGRADLVVTAPKNWLDVDTMADVD 120 L +G HLGVTGEDL+RE D D ++ LL LGFG A++VV P+ W+DV TMAD+D Sbjct: 64 THLAAGSAHLGVTGEDLIRETLSDSDRKIALLTPLGFGFANVVVAVPQAWIDVRTMADLD 123 Query: 121 EVGHAHLARTGRRLRVATKYVTQTRAFFARHGVADYRIVESSGATEGAPAAGAAELVVDI 180 +V H AR G R+RVATKY+ TR FFA V DYRIVES GATEGAPAAG AEL+VDI Sbjct: 124 DVAVLHRARRGERMRVATKYINLTRRFFASQHVTDYRIVESLGATEGAPAAGQAELIVDI 183 Query: 181 TTTGATLAANGLKILSDGVILKSQAQLTASLTAGWNGEQLDALRRLLS--VVEAKGRAGK 238 TTTGATL+AN LKIL DGVIL+S+A L ASL A WN + R +LS E +GR + Sbjct: 184 TTTGATLSANALKILDDGVILRSEANLAASLNADWNEANREKARLILSHIAAEEEGRTTR 243 Query: 239 LATLVWPAEQDRAAQDAVAAFIARGGSRRANGALLATADLFDAAAALAE----AGVEPVT 294 + V + ++A F AR +G L+ D AALA+ G V Sbjct: 244 EVSTVLENVATDSFEEAQKLFAARVRLYGKDGHLIFGCP-SDKVAALADWLIAQGASHVG 302 Query: 295 VSRPDYVFESRSAVLDRFAEAL 316 V+ DYVF +++ + ++ + L Sbjct: 303 VTAQDYVFSAKNPLYEKLVDRL 324 Lambda K H 0.318 0.133 0.375 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: 230 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: 320 Length of database: 325 Length adjustment: 28 Effective length of query: 292 Effective length of database: 297 Effective search space: 86724 Effective search space used: 86724 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_012384759.1 BIND_RS08985 (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.24333.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-58 183.0 0.4 6.8e-57 178.4 0.2 2.2 2 lcl|NCBI__GCF_000019845.1:WP_012384759.1 BIND_RS08985 ATP phosphoribosylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019845.1:WP_012384759.1 BIND_RS08985 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 178.4 0.2 6.8e-57 6.8e-57 1 182 [. 8 211 .. 8 212 .. 0.94 2 ! 2.8 0.0 0.0052 0.0052 55 78 .. 293 316 .. 232 323 .. 0.67 Alignments for each domain: == domain 1 score: 178.4 bits; conditional E-value: 6.8e-57 TIGR00070 1 lriAlp.KGrleeetlkllekaglklskke.erkliasaed.eevevlllrakdiptyvekgaadlGit 66 l +A+p KGrl+e++ +++++agl+l + + +r++ + + e+vev +++a+di+t ++ g+a+lG+t lcl|NCBI__GCF_000019845.1:WP_012384759.1 8 LVLAVPsKGRLQENVAAFFARAGLSLVQGRgSRDYRGTLKGiEGVEVAFVSASDIVTHLAAGSAHLGVT 76 679**********************999999******9888578************************* PP TIGR00070 67 GkDlleE....seadvvelldlgfgkcklvlAvpees.dvesledlke...........gkriATkypn 119 G+Dl++E s+++++ l+ lgfg +++v+Avp+++ dv++++dl++ ++r+ATky n lcl|NCBI__GCF_000019845.1:WP_012384759.1 77 GEDLIREtlsdSDRKIALLTPLGFGFANVVVAVPQAWiDVRTMADLDDvavlhrarrgeRMRVATKYIN 145 *******87666666****************************************998555******** PP TIGR00070 120 ltreylekkg.vkveivkleGavElapllgladaIvDivetGttLrengLkiie..eilessarli 182 ltr+++++++ ++++iv++ Ga+E ap++g a++IvDi++tG+tL++n Lki++ +il+s+a+l lcl|NCBI__GCF_000019845.1:WP_012384759.1 146 LTRRFFASQHvTDYRIVESLGATEGAPAAGQAELIVDITTTGATLSANALKILDdgVILRSEANLA 211 ********99789****************************************9667******996 PP == domain 2 score: 2.8 bits; conditional E-value: 0.0052 TIGR00070 55 yvekgaadlGitGkDlleEseadv 78 +++ga ++G+t +D++ ++ + lcl|NCBI__GCF_000019845.1:WP_012384759.1 293 LIAQGASHVGVTAQDYVFSAKNPL 316 4789***********998866554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (325 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: 6.29 // [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