Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate Synpcc7942_1995 Synpcc7942_1995 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >FitnessBrowser__SynE:Synpcc7942_1995 Length = 211 Score = 147 bits (372), Expect = 1e-40 Identities = 80/193 (41%), Positives = 115/193 (59%), Gaps = 6/193 (3%) Query: 17 GLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETSGNFLNVVS 76 GL+P I Q + G VLML +MN EAL+KTLE+G+V ++SR++Q LW KG TSG+F + + Sbjct: 19 GLLPAIAQDYLDGTVLMLAWMNREALEKTLETGEVWYWSRSRQELWHKGATSGHFQKLQA 78 Query: 77 IAPDCDNDTLLVLANPIGP-TCHKGTSSCFGD-----TAHQWLFLYQLEQLLAERKSADP 130 I DCD+D LL+ IG CH G SCF T L ++ +++ +R+ Sbjct: 79 IRYDCDSDALLLTIEQIGDIACHTGERSCFHRDVDVVTPPPADILTEVYRVVCDRRDRPS 138 Query: 131 ETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMYHLLVLLQDQGLD 190 E SYT+KL+A G +I +K+GEE E +A D L EA+DL +H LV L +D Sbjct: 139 EASYTSKLFAGGDNKILKKIGEEAAEVVMACKDDDADGLAGEAADLFFHTLVALAQHNVD 198 Query: 191 LTTVIENLRKRHQ 203 L +V L++R + Sbjct: 199 LRSVYRKLQERRR 211 Lambda K H 0.317 0.132 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: 118 Number of extensions: 4 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: 203 Length of database: 211 Length adjustment: 21 Effective length of query: 182 Effective length of database: 190 Effective search space: 34580 Effective search space used: 34580 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 (21.6 bits) S2: 45 (21.9 bits)
Align candidate Synpcc7942_1995 Synpcc7942_1995 (bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein)
to HMM TIGR03188 (hisE: phosphoribosyl-ATP diphosphatase (EC 3.6.1.31))
# 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/TIGR03188.hmm # target sequence database: /tmp/gapView.21926.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03188 [M=84] Accession: TIGR03188 Description: histidine_hisI: phosphoribosyl-ATP diphosphatase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-34 101.9 0.0 2.4e-33 100.5 0.0 1.6 2 lcl|FitnessBrowser__SynE:Synpcc7942_1995 Synpcc7942_1995 bifunctional pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1995 Synpcc7942_1995 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribos # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.7 0.0 0.19 0.19 44 65 .. 35 56 .. 32 58 .. 0.75 2 ! 100.5 0.0 2.4e-33 2.4e-33 1 84 [] 123 206 .. 123 206 .. 0.98 Alignments for each domain: == domain 1 score: -1.7 bits; conditional E-value: 0.19 TIGR03188 44 iiaaknedkeelveEaaDllYh 65 ++a +n++ e + E+ +++Y+ lcl|FitnessBrowser__SynE:Synpcc7942_1995 35 MLAWMNREALEKTLETGEVWYW 56 5667777777778899999997 PP == domain 2 score: 100.5 bits; conditional E-value: 2.4e-33 TIGR03188 1 leeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVl 69 l e+++v+ +r+++++e Syt+kl++ g++kilkK+gEEa+Ev++a+k++d + l+ EaaDl++h+lV+ lcl|FitnessBrowser__SynE:Synpcc7942_1995 123 LTEVYRVVCDRRDRPSEASYTSKLFAGGDNKILKKIGEEAAEVVMACKDDDADGLAGEAADLFFHTLVA 191 6799***************************************************************** PP TIGR03188 70 laekgvsledvlaeL 84 la+++v+l++v+++L lcl|FitnessBrowser__SynE:Synpcc7942_1995 192 LAQHNVDLRSVYRKL 206 ************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (211 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: 5.91 // [ok]
This GapMind analysis is from Apr 09 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