Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_029133087.1 A3GO_RS0108820 ATP phosphoribosyltransferase
Query= reanno::DvH:209044 (293 letters) >NCBI__GCF_000428045.1:WP_029133087.1 Length = 292 Score = 332 bits (852), Expect = 5e-96 Identities = 167/289 (57%), Positives = 215/289 (74%), Gaps = 2/289 (0%) Query: 7 MKLGIPKGSLEEATINLLARSGWKIRKHHRNYFPEINDPELTARLCRVQEIPRYIEDGIL 66 +KLGIPKGSLE AT++L ++GW I RNYFP IND +++ L R QE+ Y+ +G L Sbjct: 4 LKLGIPKGSLESATLSLFKQAGWNITPRSRNYFPSINDADISCALVRSQEMAPYVANGTL 63 Query: 67 DVGLTGKDWLLETGSD--VVVVSDLVYSKVSNRPARWVLAVAGDSPYTRPEDLAGKRIAT 124 D+GLTG DW+LET S+ + + +LVYSK S++P RWVL V +SP EDL GK+I+T Sbjct: 64 DLGLTGHDWILETESENELQEICELVYSKSSDQPCRWVLVVPKESPIQSIEDLQGKKIST 123 Query: 125 ELLGVTKRYFADAGIEVNVQYSWGATEAKVVEGLADAIVEVTETGTTIKAHGLRIISEVL 184 EL+ TKRY A+ G++ V++SWGATEAKVVEGL DA+VE+TETG+TIKAHGLRI+ ++L Sbjct: 124 ELVSFTKRYLAERGVQAQVEFSWGATEAKVVEGLVDAVVEITETGSTIKAHGLRIVCDIL 183 Query: 185 LTNTVLIANRAAWEDPCRRRKIEQIDLLLQGALRADSLVGLKMNVPTRCLDAVLDQLPSL 244 T T LIAN+ A +DP +R KIEQI LLQ AL A V LKMNVP L+ V+ LPSL Sbjct: 184 HTETRLIANKQAMQDPWKREKIEQIATLLQAALTARQKVALKMNVPADQLELVVGMLPSL 243 Query: 245 NSPTVAGLRDNTWFAVEIVVDNGVVRDLIPRLREAGAEGIIEYALNKVI 293 ++PTV+ L D W A+E VV++G VRDLIPRL+ AGAEGI+EY L K+I Sbjct: 244 HAPTVSHLYDQEWLAIETVVNSGEVRDLIPRLKAAGAEGILEYELRKMI 292 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: 259 Number of extensions: 10 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: 292 Length adjustment: 26 Effective length of query: 267 Effective length of database: 266 Effective search space: 71022 Effective search space used: 71022 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_029133087.1 A3GO_RS0108820 (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.2031.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-53 165.5 0.0 8.4e-53 165.0 0.0 1.2 1 lcl|NCBI__GCF_000428045.1:WP_029133087.1 A3GO_RS0108820 ATP phosphoribosy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000428045.1:WP_029133087.1 A3GO_RS0108820 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 165.0 0.0 8.4e-53 8.4e-53 1 183 [] 4 191 .. 4 191 .. 0.95 Alignments for each domain: == domain 1 score: 165.0 bits; conditional E-value: 8.4e-53 TIGR00070 1 lriAlpKGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkD 69 l++++pKG+le tl+l+++ag++++ ++ r+++ s++d+++++ l+r+++++ yv++g +dlG+tG+D lcl|NCBI__GCF_000428045.1:WP_029133087.1 4 LKLGIPKGSLESATLSLFKQAGWNITPRS-RNYFPSINDADISCALVRSQEMAPYVANGTLDLGLTGHD 71 79************************999.*************************************** PP TIGR00070 70 lleE..seadvvelldlgfgkc.....klvlAvpeesdvesledlkegkriATkypnltreylekkgvk 131 ++ E se++++e+ +l ++k+ ++vl vp+es+++s+edl+ gk+i T+ ++ t++yl+++gv+ lcl|NCBI__GCF_000428045.1:WP_029133087.1 72 WILEteSENELQEICELVYSKSsdqpcRWVLVVPKESPIQSIEDLQ-GKKISTELVSFTKRYLAERGVQ 139 ***954555599999998876444444*******************.9********************* PP TIGR00070 132 veivkleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183 +++ ++Ga+E++++ gl da+v i+etG+t++++gL+i+ +il++++rlia lcl|NCBI__GCF_000428045.1:WP_029133087.1 140 AQVEFSWGATEAKVVEGLVDAVVEITETGSTIKAHGLRIVCDILHTETRLIA 191 **************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (292 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: 7.57 // [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