Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate GFF3066 HP15_3010 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= reanno::pseudo5_N2C3_1:AO356_09800 (245 letters) >FitnessBrowser__Marino:GFF3066 Length = 245 Score = 373 bits (958), Expect = e-108 Identities = 187/245 (76%), Positives = 204/245 (83%) Query: 1 MLIIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQP 60 MLIIPAIDLKDG CVRLRQGRM+DSTVF DDPV MA +WVE G RRLHLVDLNGAF G+P Sbjct: 1 MLIIPAIDLKDGKCVRLRQGRMDDSTVFGDDPVDMATRWVEAGARRLHLVDLNGAFAGEP 60 Query: 61 VNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKEPEFVAEACRA 120 VNGE+V AIA++YP+LPIQIGGGIRS ETIE Y+KAGV +VIIGTKAVKEPEFV E C+ Sbjct: 61 VNGEIVQAIARKYPDLPIQIGGGIRSAETIEAYLKAGVQWVIIGTKAVKEPEFVTEMCKK 120 Query: 121 FPGKVIVGLDAKDGFVATDGWAEVSTVQVIDLAKRFEADGVSAIVYTDIAKDGMMQGCNV 180 FPG +IVGLDAKDG VATDGWAEVS V DLAKRF DGV AIVYTDI++DGMMQG NV Sbjct: 121 FPGHIIVGLDAKDGRVATDGWAEVSEVMATDLAKRFANDGVDAIVYTDISRDGMMQGVNV 180 Query: 181 PFTAALAAATKIPVIASGGIHNLGDIKALLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC 240 TAALA IPVIASGG+ N+ D+K L GI+GAITGRAIYEGTLDVAEAQAFC Sbjct: 181 EATAALAEEGGIPVIASGGVTNMDDLKRLATVADKGILGAITGRAIYEGTLDVAEAQAFC 240 Query: 241 DSYKG 245 D KG Sbjct: 241 DGLKG 245 Lambda K H 0.320 0.138 0.407 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: 311 Number of extensions: 6 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: 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 GFF3066 HP15_3010 (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.15575.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-85 271.0 2.1 4.9e-85 270.8 2.1 1.0 1 lcl|FitnessBrowser__Marino:GFF3066 HP15_3010 1-(5-phosphoribosyl)-5 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF3066 HP15_3010 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imida # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 270.8 2.1 4.9e-85 4.9e-85 1 230 [. 3 235 .. 3 236 .. 0.98 Alignments for each domain: == domain 1 score: 270.8 bits; conditional E-value: 4.9e-85 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveel.evk 74 iiPaiDlk+Gk+vrl qG++d +tv++ddp+++a+++ e ga++lH+VDL+gA++ge++n e+++ i+++ +++ lcl|FitnessBrowser__Marino:GFF3066 3 IIPAIDLKDGKCVRLRQGRMDDSTVFGDDPVDMATRWVEAGARRLHLVDLNGAFAGEPVNGEIVQAIARKYpDLP 77 8******************************************************************9886489* PP TIGR00007 75 vqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkekselslve 149 +q+GGGiRs+e++e++l++gv+ viigt+av++pe+v+e+ k++ +i+v+lDak+g+va+ GW+e se+ +++ lcl|FitnessBrowser__Marino:GFF3066 78 IQIGGGIRSAETIEAYLKAGVQWVIIGTKAVKEPEFVTEMCKKFP-GHIIVGLDAKDGRVATDGWAEVSEVMATD 151 ********************************************9.99*************************** PP TIGR00007 150 lakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalkk...lgvkgvivGkAl 221 lak++++ g+++i++Tdi++dG+++Gvnve+t l++e ++viasGGv++++d+k+l++ g+ g+i G+A+ lcl|FitnessBrowser__Marino:GFF3066 152 LAKRFANDGVDAIVYTDISRDGMMQGVNVEATAALAEEGGIPVIASGGVTNMDDLKRLATvadKGILGAITGRAI 226 **********************************************************9877789999******* PP TIGR00007 222 yegklklke 230 yeg+l++ e lcl|FitnessBrowser__Marino:GFF3066 227 YEGTLDVAE 235 *****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: 8.50 // [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