Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_011940835.1 GURA_RS20620 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= reanno::BFirm:BPHYT_RS17685 (250 letters) >NCBI__GCF_000016745.1:WP_011940835.1 Length = 245 Score = 279 bits (713), Expect = 4e-80 Identities = 140/246 (56%), Positives = 181/246 (73%), Gaps = 2/246 (0%) Query: 1 MLLIPAIDLKDGQCVRLKQGDMDQATIFSEEPAAMARHWVDRGARRLHLVDLNGAFAGKP 60 M++IPAIDLK+G+CVRL+QG MD+ T+F + PA AR W +G LH+VDL+GAFAGKP Sbjct: 1 MIVIPAIDLKEGKCVRLEQGLMDKDTVFCDNPAEQAREWERQGGELLHIVDLDGAFAGKP 60 Query: 61 KNEDAIRAIIEEVGGEIPVQLGGGIRDLNTIERYLDDGLSYVIIGTAAVKNPGFLQDACT 120 N+ AI AI++ V IP QLGGGIRD+ TI+ YLD GLS VI+GTAA +NP +++AC Sbjct: 61 ANKSAIEAIVKAV--RIPTQLGGGIRDIETIKAYLDLGLSRVILGTAAQRNPKLVEEACK 118 Query: 121 AFGGHIIVGLDAKDGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGIN 180 F G I+VG+DAK+G VA GW+++T DLAR FE YG ++IYTDI RDGM+QG N Sbjct: 119 LFPGRIVVGIDAKNGLVAVQGWAEVTDVYAVDLARLFEGYGVTAVIYTDISRDGMMQGPN 178 Query: 181 IEATVRLARAVKIPVIASGGLSNLTDIESLCEVEDEGIEGVICGRAIYSGDLDFAAAQTL 240 I+AT LA A+ IPVIASGG+S+L DIE+L VE G+ GVI G+AIY+G + A A L Sbjct: 179 IDATRALAEAISIPVIASGGVSSLKDIENLMAVESAGVTGVITGKAIYTGAIKLAEAVAL 238 Query: 241 ADRLRE 246 + R+ Sbjct: 239 TKKCRQ 244 Lambda K H 0.319 0.140 0.410 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: 223 Number of extensions: 14 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: 250 Length of database: 245 Length adjustment: 24 Effective length of query: 226 Effective length of database: 221 Effective search space: 49946 Effective search space used: 49946 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 (21.7 bits) S2: 46 (22.3 bits)
Align candidate WP_011940835.1 GURA_RS20620 (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.6643.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-84 268.9 1.2 2.2e-84 268.7 1.2 1.0 1 lcl|NCBI__GCF_000016745.1:WP_011940835.1 GURA_RS20620 1-(5-phosphoribosyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016745.1:WP_011940835.1 GURA_RS20620 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamin # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 268.7 1.2 2.2e-84 2.2e-84 1 230 [. 3 234 .. 3 235 .. 0.98 Alignments for each domain: == domain 1 score: 268.7 bits; conditional E-value: 2.2e-84 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 +iPaiDlkeGk+vrl qG +dk tv+ d+p+e+a+++e++g ellH+VDLdgA++g++ n+++i+ iv+ lcl|NCBI__GCF_000016745.1:WP_011940835.1 3 VIPAIDLKEGKCVRLEQGLMDKDTVFCDNPAEQAREWERQGGELLHIVDLDGAFAGKPANKSAIEAIVK 71 89******************************************************************* PP TIGR00007 70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkG 138 +++++ q+GGGiR++e+++++l+lg++rvi+gtaa +np+lv+e+ k + +ivv++Dak+g vav+G lcl|NCBI__GCF_000016745.1:WP_011940835.1 72 AVRIPTQLGGGIRDIETIKAYLDLGLSRVILGTAAQRNPKLVEEACKLFP-GRIVVGIDAKNGLVAVQG 139 *************************************************9.****************** PP TIGR00007 139 WkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkal 207 W+e +++ +v+la+ +e +g++++i+Tdi++dG+++G+n+++t+ l+++ +++viasGGvss +d+++l lcl|NCBI__GCF_000016745.1:WP_011940835.1 140 WAEVTDVYAVDLARLFEGYGVTAVIYTDISRDGMMQGPNIDATRALAEAISIPVIASGGVSSLKDIENL 208 *******************************************************************99 PP TIGR00007 208 kk...lgvkgvivGkAlyegklklke 230 + +gv+gvi GkA+y+g +kl e lcl|NCBI__GCF_000016745.1:WP_011940835.1 209 MAvesAGVTGVITGKAIYTGAIKLAE 234 8766699****************987 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.69 // [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