Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_092345231.1 BLU87_RS04765 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= reanno::HerbieS:HSERO_RS20320 (265 letters) >NCBI__GCF_900107645.1:WP_092345231.1 Length = 243 Score = 272 bits (696), Expect = 4e-78 Identities = 129/243 (53%), Positives = 180/243 (74%), Gaps = 10/243 (4%) Query: 1 MLLIPAIDLKDGHCVRLKQGDMDQATVFSEDPAEMALHWLKQGARRLHLVDLNGAFAGKP 60 M+++PAIDLK GHCVRL+QG MD+ TV+++DPA AL W +QG LH+VDL+GAFAG P Sbjct: 1 MIILPAIDLKGGHCVRLEQGLMDKDTVYNDDPAAQALLWQQQGGEFLHIVDLDGAFAGVP 60 Query: 61 KNEAAVKAILKAVASFAEENEVEEIPVQLGGGIRDLDTIERYLDDGLSYIIIGTAAVKNP 120 KN++A+++I+ A+ IP +LGGGIRDL+TIE YLD G++ +I+GT A +NP Sbjct: 61 KNKSAIQSIVNAI----------NIPSELGGGIRDLETIEAYLDLGITRVILGTVAKENP 110 Query: 121 GFLHDACSAFPGQIIVGLDAKDGKVATDGWSKLSGHEVVDLAQKFEGYGCEAIVYTDIGR 180 + +AC FPGQI+VG+DAKDG VA GW+ ++ + ++A++ EG+G EAI+YTDI R Sbjct: 111 ALVKEACRKFPGQIVVGIDAKDGLVAVRGWADVTEKKATEMAKEMEGFGVEAIIYTDISR 170 Query: 181 DGMMGGVNIEATVRLAQAVTIPIIASGGVHNVGDVEALCRVEDEGIEAVICGRSIYEGTL 240 DGMM G NIEAT LA+A+ IP+IASGG+ + D+ L ++E G+ VI G++IY G + Sbjct: 171 DGMMQGPNIEATRALAEAIIIPVIASGGLSTLDDIRKLLQIESSGVTGVITGKAIYSGAI 230 Query: 241 DLR 243 DLR Sbjct: 231 DLR 233 Lambda K H 0.318 0.138 0.400 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: 258 Number of extensions: 11 Number of successful extensions: 4 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: 265 Length of database: 243 Length adjustment: 24 Effective length of query: 241 Effective length of database: 219 Effective search space: 52779 Effective search space used: 52779 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: 47 (22.7 bits)
Align candidate WP_092345231.1 BLU87_RS04765 (1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase)
to HMM TIGR00007 (hisA: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16))
# 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/TIGR00007.hmm # target sequence database: /tmp/gapView.11255.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00007 [M=231] Accession: TIGR00007 Description: TIGR00007: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase 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-82 262.7 1.3 1.7e-82 262.5 1.3 1.0 1 lcl|NCBI__GCF_900107645.1:WP_092345231.1 BLU87_RS04765 1-(5-phosphoribosy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900107645.1:WP_092345231.1 BLU87_RS04765 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneami # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 262.5 1.3 1.7e-82 1.7e-82 1 230 [. 3 234 .. 3 235 .. 0.98 Alignments for each domain: == domain 1 score: 262.5 bits; conditional E-value: 1.7e-82 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 i+PaiDlk G++vrl qG +dk tvy+ddp+++a ++++g e+lH+VDLdgA++g +kn+++i++iv+ lcl|NCBI__GCF_900107645.1:WP_092345231.1 3 ILPAIDLKGGHCVRLEQGLMDKDTVYNDDPAAQALLWQQQGGEFLHIVDLDGAFAGVPKNKSAIQSIVN 71 89******************************************************************* PP TIGR00007 70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkG 138 +++++ ++GGGiR+le++e++l+lg++rvi+gt+a enp+lvke+ +++ +ivv++Dak+g vav+G lcl|NCBI__GCF_900107645.1:WP_092345231.1 72 AINIPSELGGGIRDLETIEAYLDLGITRVILGTVAKENPALVKEACRKFP-GQIVVGIDAKDGLVAVRG 139 *************************************************9.99**************** PP TIGR00007 139 WkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkal 207 W++ +e +++e+ak++e +g+e+ii+Tdi++dG+++G+n+e+t+ l+++ ++viasGG s+ +d+++l lcl|NCBI__GCF_900107645.1:WP_092345231.1 140 WADVTEKKATEMAKEMEGFGVEAIIYTDISRDGMMQGPNIEATRALAEAIIIPVIASGGLSTLDDIRKL 208 *******************************************************************99 PP TIGR00007 208 kk...lgvkgvivGkAlyegklklke 230 + +gv+gvi GkA+y+g ++l+e lcl|NCBI__GCF_900107645.1:WP_092345231.1 209 LQiesSGVTGVITGKAIYSGAIDLRE 234 8766699***************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (243 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: 7.93 // [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