Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_012506540.1 PAES_RS09960 ATP phosphoribosyltransferase
Query= reanno::DvH:209044 (293 letters) >NCBI__GCF_000020625.1:WP_012506540.1 Length = 294 Score = 312 bits (799), Expect = 7e-90 Identities = 155/287 (54%), Positives = 208/287 (72%), Gaps = 1/287 (0%) Query: 7 MKLGIPKGSLEEATINLLARSGWKIRKHHRNYFPEINDPELTARLCRVQEIPRYIEDGIL 66 +KLG+PKGSL+++T++L A++G+ R+YFP I+D EL A L R QE+ Y+E G Sbjct: 8 LKLGLPKGSLQDSTLDLFAKAGFHFSVKSRSYFPSIDDDELEAILIRAQEMAHYVELGAF 67 Query: 67 DVGLTGKDWLLETGSDVVVVSDLVYSKVSNRPARWVLAVAGDSPYTRPEDLAGKRIATEL 126 DVGLTGKDW++ET +DVV VSDLVYSK S RP RWVLAV S +DL GK IATE+ Sbjct: 68 DVGLTGKDWIIETDADVVEVSDLVYSKASMRPVRWVLAVPESSSIQTVKDLEGKHIATEV 127 Query: 127 LGVTKRYFADAGIEVNVQYSWGATEAKVVEGLADAIVEVTETGTTIKAHGLRIISEVLLT 186 + +TK+Y A+ + +V++SWGATE K E LADAIVEVTETG++++A+ LRI+ +L + Sbjct: 128 VNITKKYLAENNVNAHVEFSWGATEVKPPE-LADAIVEVTETGSSLRANKLRIVEVLLES 186 Query: 187 NTVLIANRAAWEDPCRRRKIEQIDLLLQGALRADSLVGLKMNVPTRCLDAVLDQLPSLNS 246 NT LIANR +W DP +R KIE + +LLQGA+ A VGLKMN P LD ++ +P L + Sbjct: 187 NTKLIANRNSWNDPWKREKIENMAMLLQGAIHAQGKVGLKMNAPKDALDKIMAFIPGLRT 246 Query: 247 PTVAGLRDNTWFAVEIVVDNGVVRDLIPRLREAGAEGIIEYALNKVI 293 PTV+ L D+ W A+E++VD VR +IP L+ AGAEGI EY +NK+I Sbjct: 247 PTVSNLADDKWVALEVIVDEQTVRSVIPDLKRAGAEGIFEYHINKLI 293 Lambda K H 0.319 0.137 0.402 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: 256 Number of extensions: 6 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: 293 Length of database: 294 Length adjustment: 26 Effective length of query: 267 Effective length of database: 268 Effective search space: 71556 Effective search space used: 71556 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_012506540.1 PAES_RS09960 (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.2605.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-58 183.1 0.0 3.1e-58 182.7 0.0 1.1 1 lcl|NCBI__GCF_000020625.1:WP_012506540.1 PAES_RS09960 ATP phosphoribosylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020625.1:WP_012506540.1 PAES_RS09960 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 182.7 0.0 3.1e-58 3.1e-58 1 183 [] 8 192 .. 8 192 .. 0.98 Alignments for each domain: == domain 1 score: 182.7 bits; conditional E-value: 3.1e-58 TIGR00070 1 lriAlpKGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkD 69 l+++lpKG+l+++tl+l++kag+++s k+ r+++ s++d+e+e++l+ra++++ yve ga+d+G+tGkD lcl|NCBI__GCF_000020625.1:WP_012506540.1 8 LKLGLPKGSLQDSTLDLFAKAGFHFSVKS-RSYFPSIDDDELEAILIRAQEMAHYVELGAFDVGLTGKD 75 79***************************.*************************************** PP TIGR00070 70 lleEseadvvelldlgfgkc.....klvlAvpeesdvesledlkegkriATkypnltreylekkgvkve 133 ++ E +advve+ dl ++k+ ++vlAvpe+s++++++dl+ gk iAT+ +n+t++yl++++v+++ lcl|NCBI__GCF_000020625.1:WP_012506540.1 76 WIIETDADVVEVSDLVYSKAsmrpvRWVLAVPESSSIQTVKDLE-GKHIATEVVNITKKYLAENNVNAH 143 ***************99999888889******************.9*********************** PP TIGR00070 134 ivkleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183 + ++Ga+E++p +ladaIv ++etG++Lr+n+L+i+e++les+++lia lcl|NCBI__GCF_000020625.1:WP_012506540.1 144 VEFSWGATEVKP-PELADAIVEVTETGSSLRANKLRIVEVLLESNTKLIA 192 ************.89*********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (294 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: 7.35 // [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