Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate Ac3H11_4732 Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)
Query= reanno::BFirm:BPHYT_RS17685 (250 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4732 Length = 246 Score = 413 bits (1061), Expect = e-120 Identities = 202/244 (82%), Positives = 222/244 (90%) Query: 1 MLLIPAIDLKDGQCVRLKQGDMDQATIFSEEPAAMARHWVDRGARRLHLVDLNGAFAGKP 60 MLLIPAIDLKDG CVRLKQGDMDQ+T F E+PAAMAR WVD GARRLHLVDLNGAFAG P Sbjct: 1 MLLIPAIDLKDGHCVRLKQGDMDQSTTFGEDPAAMARKWVDAGARRLHLVDLNGAFAGVP 60 Query: 61 KNEDAIRAIIEEVGGEIPVQLGGGIRDLNTIERYLDDGLSYVIIGTAAVKNPGFLQDACT 120 KN AI++I++EVG +IPVQLGGGIRDL+TIE+Y+D GL YVIIGTAAVKNPGFL+DAC+ Sbjct: 61 KNYGAIKSILKEVGSDIPVQLGGGIRDLDTIEKYIDGGLRYVIIGTAAVKNPGFLKDACS 120 Query: 121 AFGGHIIVGLDAKDGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGIN 180 AFGGHIIVGLDAKDGKVATDGWSKLTGHEV DLA+KFED+G ESIIYTDIGRDGML GIN Sbjct: 121 AFGGHIIVGLDAKDGKVATDGWSKLTGHEVVDLAKKFEDWGVESIIYTDIGRDGMLSGIN 180 Query: 181 IEATVRLARAVKIPVIASGGLSNLTDIESLCEVEDEGIEGVICGRAIYSGDLDFAAAQTL 240 I+ATV+LA+A+ IPVIASGGLSN+ DIE LC VE EG+EGVICGRAIYSGDLDFAAAQ Sbjct: 181 IDATVKLAQALSIPVIASGGLSNMADIEQLCAVESEGVEGVICGRAIYSGDLDFAAAQAR 240 Query: 241 ADRL 244 AD L Sbjct: 241 ADEL 244 Lambda K H 0.319 0.140 0.410 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: 338 Number of extensions: 8 Number of successful extensions: 1 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: 250 Length of database: 246 Length adjustment: 24 Effective length of query: 226 Effective length of database: 222 Effective search space: 50172 Effective search space used: 50172 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: 46 (22.3 bits)
Align candidate Ac3H11_4732 (Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16))
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.20782.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-81 257.2 0.6 8.2e-81 257.0 0.6 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4732 Phosphoribosylformimino-5-aminoi Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4732 Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomer # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.0 0.6 8.2e-81 8.2e-81 1 229 [. 3 235 .. 3 237 .. 0.97 Alignments for each domain: == domain 1 score: 257.0 bits; conditional E-value: 8.2e-81 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknle 62 +iPaiDlk+G++vrl qGd+d++t++++dp+++a+k+ + ga++lH+VDL+gA++g +kn lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4732 3 LIPAIDLKDGHCVRLKQGDMDQSTTFGEDPAAMARKWVDAGARRLHLVDLNGAFAGVPKNYG 64 59************************************************************ PP TIGR00007 63 vikkiveel..evkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsek 122 +ik+i++e+ +++vq+GGGiR+l+++ek+++ g+++viigtaav+np ++k++ +++g + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4732 65 AIKSILKEVgsDIPVQLGGGIRDLDTIEKYIDGGLRYVIIGTAAVKNPGFLKDACSAFG-GH 125 *******98335789********************************************.99 PP TIGR00007 123 ivvslDakegevavkGWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkel 184 i+v+lDak+g+va+ GW + + ++v+lakk+e+ g+e+ii+Tdi +dG+lsG+n+++t +l lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4732 126 IIVGLDAKDGKVATDGWSKLTGHEVVDLAKKFEDWGVESIIYTDIGRDGMLSGINIDATVKL 187 ************************************************************** PP TIGR00007 185 vkeaeveviasGGvssiedvkalkk...lgvkgvivGkAlyegklklk 229 +++ +++viasGG s+++d+++l + gv+gvi+G+A+y+g+l++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4732 188 AQALSIPVIASGGLSNMADIEQLCAvesEGVEGVICGRAIYSGDLDFA 235 *********************997755589**************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (246 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: 9.70 // [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