Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_028487400.1 B076_RS0111215 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= reanno::psRCH2:GFF155 (247 letters) >NCBI__GCF_000483485.1:WP_028487400.1 Length = 247 Score = 333 bits (853), Expect = 3e-96 Identities = 163/241 (67%), Positives = 192/241 (79%) Query: 1 MLIIPAIDLKDGACVRLRQGLMDDATVFSDDPVAMAAKWVEAGCRRLHLVDLNGAFEGQP 60 ML+IPAIDLKDG CVRLRQG+M+DATVFS D VAMA +WV+ G RRLH+VDLNGAFEG+P Sbjct: 1 MLLIPAIDLKDGQCVRLRQGIMEDATVFSGDIVAMAERWVDQGARRLHMVDLNGAFEGKP 60 Query: 61 VNGEVVTAIAKRYPDLPIQIGGGIRTLETIEHYVRAGVSYVIIGTKAVKEPGFVTEACRA 120 VNGE V + + YPDLPIQIGGGIR L+TIE Y+ AGVSY IIGTKAV P FV EAC+A Sbjct: 61 VNGEAVYQVREAYPDLPIQIGGGIRDLQTIEAYLNAGVSYCIIGTKAVHNPEFVAEACQA 120 Query: 121 FPGKVIVGLDAKDGFVATDGWAEVSSVQAVDLARRFEADGVSAIVYTDIAKDGMMQGCNV 180 FPG ++VGLDAK+G VA +GWAEV+ + L ++FE DGV AI+YTDI +DGMMQG N+ Sbjct: 121 FPGHIMVGLDAKEGMVAINGWAEVTDHEVTQLGKQFENDGVEAIIYTDIGRDGMMQGVNI 180 Query: 181 EATVALANASRIPVIASGGIHNIGDIQKLLDTNTPGIVGAITGRAIYEGTLDVAEAQALC 240 EAT ALA A IP+IASGGI N+ DI++L G+ GAITGRAIYEG+LD E QAL Sbjct: 181 EATQALAKALNIPIIASGGITNLDDIRRLASIEADGVSGAITGRAIYEGSLDFKEGQALS 240 Query: 241 D 241 D Sbjct: 241 D 241 Lambda K H 0.320 0.138 0.405 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: 285 Number of extensions: 12 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: 247 Length of database: 247 Length adjustment: 24 Effective length of query: 223 Effective length of database: 223 Effective search space: 49729 Effective search space used: 49729 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_028487400.1 B076_RS0111215 (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.487.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-81 257.8 1.0 5.4e-81 257.6 1.0 1.0 1 lcl|NCBI__GCF_000483485.1:WP_028487400.1 B076_RS0111215 1-(5-phosphoribos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000483485.1:WP_028487400.1 B076_RS0111215 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneam # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.6 1.0 5.4e-81 5.4e-81 1 230 [. 3 235 .. 3 236 .. 0.97 Alignments for each domain: == domain 1 score: 257.6 bits; conditional E-value: 5.4e-81 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 +iPaiDlk+G++vrl qG ++ tv+s d++++a+++ ++ga++lH+VDL+gA+eg+++n e++ ++ e lcl|NCBI__GCF_000483485.1:WP_028487400.1 3 LIPAIDLKDGQCVRLRQGIMEDATVFSGDIVAMAERWVDQGARRLHMVDLNGAFEGKPVNGEAVYQVRE 71 59******************************************************************9 PP TIGR00007 70 el.evkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavk 137 + ++++q+GGGiR+l+++e++l++gv+++iigt+av+npe+v+e+ +++ +i+v+lDakeg va++ lcl|NCBI__GCF_000483485.1:WP_028487400.1 72 AYpDLPIQIGGGIRDLQTIEAYLNAGVSYCIIGTKAVHNPEFVAEACQAFP-GHIMVGLDAKEGMVAIN 139 86489*********************************************9.99*************** PP TIGR00007 138 GWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvka 206 GW+e ++ ++++l k++e+ g+e+ii+Tdi +dG+++Gvn+e+t+ l+k+ ++++iasGG+++ +d+++ lcl|NCBI__GCF_000483485.1:WP_028487400.1 140 GWAEVTDHEVTQLGKQFENDGVEAIIYTDIGRDGMMQGVNIEATQALAKALNIPIIASGGITNLDDIRR 208 ********************************************************************* PP TIGR00007 207 lkk...lgvkgvivGkAlyegklklke 230 l++ gv+g+i G+A+yeg+l++ke lcl|NCBI__GCF_000483485.1:WP_028487400.1 209 LASieaDGVSGAITGRAIYEGSLDFKE 235 *9966678899************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (247 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: 8.59 // [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