Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_010962004.1 MCA_RS13725 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= reanno::Putida:PP_0292 (245 letters) >NCBI__GCF_000008325.1:WP_010962004.1 Length = 243 Score = 305 bits (781), Expect = 5e-88 Identities = 151/243 (62%), Positives = 184/243 (75%) Query: 1 MLIIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQP 60 ML+IPAIDLKDG CVRLRQGRMED TVFSDDPV++A +WV G RRLHLVDL+GAF G+P Sbjct: 1 MLLIPAIDLKDGKCVRLRQGRMEDDTVFSDDPVAVAGRWVAAGARRLHLVDLDGAFAGKP 60 Query: 61 VNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKQPEFVAEACKA 120 N E + AI + P++ IQ+GGGIR ETI+ Y+ AGV +VIIGTKAV P FV++ Sbjct: 61 RNAETIHAIREACPDVEIQVGGGIRDEETIQGYLNAGVDFVIIGTKAVSAPHFVSDVTAE 120 Query: 121 FPGKVIVGLDAKDGFVATDGWAEVSSVQVIDLAKRFEADGVSAIVYTDIAKDGMMQGCNV 180 FP +I+GLDA+DG VA DGW+++S VIDLA++FEADGV AI+YTDI++DGMM G N+ Sbjct: 121 FPNHIIIGLDARDGKVAIDGWSKLSHHDVIDLAQKFEADGVEAIIYTDISRDGMMGGVNI 180 Query: 181 PFTKALAEATRIPVIASGGIHNLGDIKALLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC 240 T LA A IPVIASGGI + DIKAL + G+IGAITGRAIYEGTLD AE Sbjct: 181 EATSRLARAIHIPVIASGGITTIDDIKALGEIVGDGVIGAITGRAIYEGTLDFAEGLKLA 240 Query: 241 DNY 243 + + Sbjct: 241 ETF 243 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: 272 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: 243 Length adjustment: 24 Effective length of query: 221 Effective length of database: 219 Effective search space: 48399 Effective search space used: 48399 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 WP_010962004.1 MCA_RS13725 (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.24652.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-80 256.3 2.1 1.5e-80 256.1 2.1 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010962004.1 MCA_RS13725 1-(5-phosphoribosyl) Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010962004.1 MCA_RS13725 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 256.1 2.1 1.5e-80 1.5e-80 1 229 [. 3 234 .. 3 236 .. 0.98 Alignments for each domain: == domain 1 score: 256.1 bits; conditional E-value: 1.5e-80 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 +iPaiDlk+Gk+vrl qG+++ tv+sddp+++a ++ + ga++lH+VDLdgA++g+++n+e+i+ i e lcl|NCBI__GCF_000008325.1:WP_010962004.1 3 LIPAIDLKDGKCVRLRQGRMEDDTVFSDDPVAVAGRWVAAGARRLHLVDLDGAFAGKPRNAETIHAIRE 71 59******************************************************************9 PP TIGR00007 70 el.evkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavk 137 ++ +v++qvGGGiR+ e+++ +l++gv+ viigt+av+ p++v+++ +e+ ++i+++lDa++g+va+ lcl|NCBI__GCF_000008325.1:WP_010962004.1 72 ACpDVEIQVGGGIRDEETIQGYLNAGVDFVIIGTKAVSAPHFVSDVTAEFP-NHIIIGLDARDGKVAID 139 98579*********************************************9.99*************** PP TIGR00007 138 GWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvka 206 GW + s+ ++++la+k+e g+e+ii+Tdi++dG++ Gvn+e+t++l+++ +++viasGG+++i+d+ka lcl|NCBI__GCF_000008325.1:WP_010962004.1 140 GWSKLSHHDVIDLAQKFEADGVEAIIYTDISRDGMMGGVNIEATSRLARAIHIPVIASGGITTIDDIKA 208 ********************************************************************* PP TIGR00007 207 lkk...lgvkgvivGkAlyegklklk 229 l + gv g+i G+A+yeg+l++ lcl|NCBI__GCF_000008325.1:WP_010962004.1 209 LGEivgDGVIGAITGRAIYEGTLDFA 234 *9988789999***********9976 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: 6.31 // [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