Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_028320632.1 H567_RS0105470 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= reanno::psRCH2:GFF155 (247 letters) >NCBI__GCF_000422285.1:WP_028320632.1 Length = 244 Score = 254 bits (648), Expect = 1e-72 Identities = 124/236 (52%), Positives = 168/236 (71%), Gaps = 1/236 (0%) Query: 1 MLIIPAIDLKDGACVRLRQGLMDDATVFSDDPVAMAAKWVEAGCRRLHLVDLNGAFEGQP 60 M+IIPAID+K G CVRL+QGLM TVFS+ P MA +WV+ G +RLH+VDL+GA +G+P Sbjct: 1 MIIIPAIDIKGGRCVRLQQGLMSKETVFSNFPEEMAQRWVDKGAQRLHIVDLDGAVQGRP 60 Query: 61 VNGEVVTAIAKRYPDLPIQIGGGIRTLETIEHYVRAGVSYVIIGTKAVKEPGFVTEACRA 120 VN E + I K +P+++GGGIR T++ Y G++Y I+GT A+K P FV EAC A Sbjct: 61 VNAETIARIVKA-ARIPVELGGGIRDFATLKAYFDLGIAYAILGTVALKNPDFVKEACNA 119 Query: 121 FPGKVIVGLDAKDGFVATDGWAEVSSVQAVDLARRFEADGVSAIVYTDIAKDGMMQGCNV 180 FPGK+I+G+DA+ VA +GW E + ++LAR+F ++AI+YTDI +DGM G N Sbjct: 120 FPGKIILGIDARGNRVAAEGWTEEFAETPLELARKFGPFNLAAIIYTDIFRDGMRTGPNT 179 Query: 181 EATVALANASRIPVIASGGIHNIGDIQKLLDTNTPGIVGAITGRAIYEGTLDVAEA 236 EAT ALA A PVIASGGI +I +++LL G++G ITGRA+Y+GTLD+ EA Sbjct: 180 EATRALARALDTPVIASGGIADISHVEELLQIEKDGVIGMITGRALYDGTLDIEEA 235 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: 217 Number of extensions: 11 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: 247 Length of database: 244 Length adjustment: 24 Effective length of query: 223 Effective length of database: 220 Effective search space: 49060 Effective search space used: 49060 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_028320632.1 H567_RS0105470 (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.10117.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-78 247.0 0.0 1.1e-77 246.8 0.0 1.0 1 lcl|NCBI__GCF_000422285.1:WP_028320632.1 H567_RS0105470 1-(5-phosphoribos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000422285.1:WP_028320632.1 H567_RS0105470 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneam # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 246.8 0.0 1.1e-77 1.1e-77 1 231 [] 3 235 .. 3 235 .. 0.97 Alignments for each domain: == domain 1 score: 246.8 bits; conditional E-value: 1.1e-77 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 iiPaiD+k G++vrl+qG ++k+tv+s+ p+e+a+++ ++ga++lH+VDLdgA +g+++n+e+i++iv+ lcl|NCBI__GCF_000422285.1:WP_028320632.1 3 IIPAIDIKGGRCVRLQQGLMSKETVFSNFPEEMAQRWVDKGAQRLHIVDLDGAVQGRPVNAETIARIVK 71 8******************************************************************** PP TIGR00007 70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkG 138 +++++v++GGGiR++++++++++lg+++ i+gt+a++np++vke+ +++ ki++++Da++++va +G lcl|NCBI__GCF_000422285.1:WP_028320632.1 72 AARIPVELGGGIRDFATLKAYFDLGIAYAILGTVALKNPDFVKEACNAFP-GKIILGIDARGNRVAAEG 139 *************************************************9.9***************** PP TIGR00007 139 WkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkal 207 W+e+ +++ela+k+ ++l++ii+Tdi +dG+ +G+n+e+t+ l+++ +++viasGG+++i+ v++l lcl|NCBI__GCF_000422285.1:WP_028320632.1 140 WTEEFAETPLELARKFGPFNLAAIIYTDIFRDGMRTGPNTEATRALARALDTPVIASGGIADISHVEEL 208 **************************************************************9999988 PP TIGR00007 208 kk...lgvkgvivGkAlyegklklkea 231 + gv g+i G+Aly+g+l+++ea lcl|NCBI__GCF_000422285.1:WP_028320632.1 209 LQiekDGVIGMITGRALYDGTLDIEEA 235 773337777889**********99985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (244 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.12 // [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