Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate PfGW456L13_359 Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_359 (245 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_359 Length = 245 Score = 487 bits (1253), Expect = e-142 Identities = 245/245 (100%), Positives = 245/245 (100%) Query: 1 MLIIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQP 60 MLIIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQP Sbjct: 1 MLIIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQP 60 Query: 61 VNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKDPAFVAEACRA 120 VNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKDPAFVAEACRA Sbjct: 61 VNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKDPAFVAEACRA 120 Query: 121 FPGKIIVGLDAKDGFVATDGWAEISTIQVIDLAKQFEADGVSSIVYTDIAKDGMMQGCNV 180 FPGKIIVGLDAKDGFVATDGWAEISTIQVIDLAKQFEADGVSSIVYTDIAKDGMMQGCNV Sbjct: 121 FPGKIIVGLDAKDGFVATDGWAEISTIQVIDLAKQFEADGVSSIVYTDIAKDGMMQGCNV 180 Query: 181 PFTAALAAATKIPVIASGGIHNLGDIKTLLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC 240 PFTAALAAATKIPVIASGGIHNLGDIKTLLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC Sbjct: 181 PFTAALAAATKIPVIASGGIHNLGDIKTLLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC 240 Query: 241 DSYKG 245 DSYKG Sbjct: 241 DSYKG 245 Lambda K H 0.320 0.138 0.408 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: 405 Number of extensions: 7 Number of successful extensions: 3 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: 245 Length of database: 245 Length adjustment: 24 Effective length of query: 221 Effective length of database: 221 Effective search space: 48841 Effective search space used: 48841 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 (21.8 bits) S2: 46 (22.3 bits)
Align candidate PfGW456L13_359 (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.158600.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-81 257.3 0.4 7.5e-81 257.1 0.4 1.0 1 FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_359 Domain annotation for each sequence (and alignments): >> FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_359 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.1 0.4 7.5e-81 7.5e-81 1 230 [. 3 235 .. 3 236 .. 0.96 Alignments for each domain: == domain 1 score: 257.1 bits; conditional E-value: 7.5e-81 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekkn 60 iiPaiDlk+G++vrl qG+++ +tv+sddp+ +a+k+ e g ++lH+VDL+gA+eg+++n FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_359 3 IIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQPVN 62 8*********************************************************** PP TIGR00007 61 levikkiveel.evkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelg 119 ev+ i+++ ++++q+GGGiRsle++e+++++gv++viigt+av++p++v+e+ +++ FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_359 63 GEVVTAIAKRYpNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKDPAFVAEACRAFP 122 *******9876489*********************************************9 PP TIGR00007 120 sekivvslDakegevavkGWkekselslvelakkleelgleeiilTdiekdGtlsGvnve 179 ki+v+lDak+g va+ GW+e s++++++lak++e g+++i++Tdi+kdG+++G nv FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_359 123 -GKIIVGLDAKDGFVATDGWAEISTIQVIDLAKQFEADGVSSIVYTDIAKDGMMQGCNVP 181 .9********************************************************** PP TIGR00007 180 ltkelvkeaeveviasGGvssiedvkalkk...lgvkgvivGkAlyegklklke 230 t l+++++++viasGG+++ d+k+l + g+ g+i G+A+yeg+l++ e FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_359 182 FTAALAAATKIPVIASGGIHNLGDIKTLLDakaPGIIGAITGRAIYEGTLDVAE 235 **************************9866333788889***********9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (245 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: 17.30 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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