Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_013554618.1 NITSA_RS08550 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= reanno::psRCH2:GFF155 (247 letters) >NCBI__GCF_000186245.1:WP_013554618.1 Length = 239 Score = 230 bits (587), Expect = 2e-65 Identities = 121/236 (51%), Positives = 165/236 (69%), Gaps = 6/236 (2%) Query: 1 MLIIPAIDLKDGACVRLRQGLMDDATVFSDDPVAMAAKWVEAGCRRLHLVDLNGAFEGQP 60 M+I+PAIDLKDG VRL +GLMD A ++SD+P +A + E G LHLVDLNGAF G+P Sbjct: 1 MIILPAIDLKDGKAVRLSKGLMDSAKIYSDEPWQVAKHFEELGSEWLHLVDLNGAFAGEP 60 Query: 61 VNGEVVTAIAKRYPDLPIQIGGGIRTLETIEHYVRAGVSYVIIGTKAVKEPGFVTEACRA 120 N E + I + +L +++GGGIR ETI Y+ GV +I+G+ AVK+P FV + Sbjct: 61 KNLEQIRKIRENC-NLKLELGGGIRDEETIRMYLDLGVDRLILGSVAVKDPDFVRKMAAK 119 Query: 121 FPGKVIVGLDAKDGFVATDGWAEVSSVQAVDLARRFEADGVSAIVYTDIAKDGMMQGCNV 180 +P ++VG+DA DG VA +GWAEVS ++A DLAR F GV AI+ TD+ +DGM+ G NV Sbjct: 120 YP--IVVGIDAIDGMVAVEGWAEVSEMKATDLARAFADAGVEAIICTDVGRDGMLSGINV 177 Query: 181 EATVALANASRIPVIASGGIHNIGDIQKLLDTNTPGIVGAITGRAIYEGTLDVAEA 236 E T ++A+AS +P IASGG+ +I DI++L++ GI G I G+A YEGTLD+ EA Sbjct: 178 EFTRSIAHASGLPTIASGGLRDIEDIRRLIEA---GIYGTIVGKAFYEGTLDLEEA 230 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: 216 Number of extensions: 9 Number of successful extensions: 5 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: 239 Length adjustment: 23 Effective length of query: 224 Effective length of database: 216 Effective search space: 48384 Effective search space used: 48384 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_013554618.1 NITSA_RS08550 (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.26894.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.1e-86 273.2 0.1 1e-85 273.0 0.1 1.0 1 lcl|NCBI__GCF_000186245.1:WP_013554618.1 NITSA_RS08550 1-(5-phosphoribosy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013554618.1 NITSA_RS08550 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneami # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 273.0 0.1 1e-85 1e-85 1 231 [] 3 230 .. 3 230 .. 0.99 Alignments for each domain: == domain 1 score: 273.0 bits; conditional E-value: 1e-85 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 i+PaiDlk+Gk+vrl +G +d+ ++ysd+p+++ak+fee g e+lH+VDL+gA++ge+knle i+ki e lcl|NCBI__GCF_000186245.1:WP_013554618.1 3 ILPAIDLKDGKAVRLSKGLMDSAKIYSDEPWQVAKHFEELGSEWLHLVDLNGAFAGEPKNLEQIRKIRE 71 89******************************************************************* PP TIGR00007 70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkG 138 ++++k+++GGGiR+ e+++ +l+lgv+r+i+g++av++p++v+++++++ ivv++Da +g vav+G lcl|NCBI__GCF_000186245.1:WP_013554618.1 72 NCNLKLELGGGIRDEETIRMYLDLGVDRLILGSVAVKDPDFVRKMAAKYP---IVVGIDAIDGMVAVEG 137 *************************************************9...**************** PP TIGR00007 139 WkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkal 207 W+e se+++++la+ ++++g+e+ii+Td+ +dG+lsG+nve t+++++++ + iasGG ++ied+++l lcl|NCBI__GCF_000186245.1:WP_013554618.1 138 WAEVSEMKATDLARAFADAGVEAIICTDVGRDGMLSGINVEFTRSIAHASGLPTIASGGLRDIEDIRRL 206 ********************************************************************* PP TIGR00007 208 kklgvkgvivGkAlyegklklkea 231 ++g++g ivGkA+yeg+l+l+ea lcl|NCBI__GCF_000186245.1:WP_013554618.1 207 IEAGIYGTIVGKAFYEGTLDLEEA 230 ********************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (239 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: 6.70 // [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