Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_012402124.1 BPHY_RS14005 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= reanno::BFirm:BPHYT_RS17685 (250 letters) >NCBI__GCF_000020045.1:WP_012402124.1 Length = 250 Score = 483 bits (1242), Expect = e-141 Identities = 242/250 (96%), Positives = 244/250 (97%) Query: 1 MLLIPAIDLKDGQCVRLKQGDMDQATIFSEEPAAMARHWVDRGARRLHLVDLNGAFAGKP 60 MLLIPAIDLKDGQCVRLKQGDMDQATIF EEPA MARHWVDRGARRLHLVDLNGAFAGKP Sbjct: 1 MLLIPAIDLKDGQCVRLKQGDMDQATIFHEEPAVMARHWVDRGARRLHLVDLNGAFAGKP 60 Query: 61 KNEDAIRAIIEEVGGEIPVQLGGGIRDLNTIERYLDDGLSYVIIGTAAVKNPGFLQDACT 120 KNEDAIRAIIEEVGGEIPVQLGGGIRDLNTIERYLDDGL YVIIGTAAVKNPGFL +ACT Sbjct: 61 KNEDAIRAIIEEVGGEIPVQLGGGIRDLNTIERYLDDGLEYVIIGTAAVKNPGFLLEACT 120 Query: 121 AFGGHIIVGLDAKDGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGIN 180 AFGGHIIVGLDAKDGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGIN Sbjct: 121 AFGGHIIVGLDAKDGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGIN 180 Query: 181 IEATVRLARAVKIPVIASGGLSNLTDIESLCEVEDEGIEGVICGRAIYSGDLDFAAAQTL 240 IEATVRLARAVKIPVIASGGLSNL DIE+LCEVEDEGIEGVICGRAIYSGDLDFAAAQT Sbjct: 181 IEATVRLARAVKIPVIASGGLSNLGDIEALCEVEDEGIEGVICGRAIYSGDLDFAAAQTH 240 Query: 241 ADRLRESDDA 250 ADRLRESDDA Sbjct: 241 ADRLRESDDA 250 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: 380 Number of extensions: 3 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: 250 Length of database: 250 Length adjustment: 24 Effective length of query: 226 Effective length of database: 226 Effective search space: 51076 Effective search space used: 51076 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_012402124.1 BPHY_RS14005 (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.20099.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-81 258.2 0.3 4.1e-81 258.0 0.3 1.0 1 lcl|NCBI__GCF_000020045.1:WP_012402124.1 BPHY_RS14005 1-(5-phosphoribosyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020045.1:WP_012402124.1 BPHY_RS14005 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamin # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 258.0 0.3 4.1e-81 4.1e-81 1 229 [. 3 235 .. 3 237 .. 0.97 Alignments for each domain: == domain 1 score: 258.0 bits; conditional E-value: 4.1e-81 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 +iPaiDlk+G++vrl qGd+d+ t+++++p+ +a+++ + ga++lH+VDL+gA++g++kn+++i+ i+e lcl|NCBI__GCF_000020045.1:WP_012402124.1 3 LIPAIDLKDGQCVRLKQGDMDQATIFHEEPAVMARHWVDRGARRLHLVDLNGAFAGKPKNEDAIRAIIE 71 59******************************************************************* PP TIGR00007 70 el..evkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevav 136 e+ e++vq+GGGiR+l+++e++l+ g+e+viigtaav+np ++ e+ +++g +i+v+lDak+g+va+ lcl|NCBI__GCF_000020045.1:WP_012402124.1 72 EVggEIPVQLGGGIRDLNTIERYLDDGLEYVIIGTAAVKNPGFLLEACTAFG-GHIIVGLDAKDGKVAT 139 99445789********************************************.99************** PP TIGR00007 137 kGWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvk 205 GW + + ++++la+k+e++g+e+ii+Tdi +dG+l+G+n+e+t +l+++++++viasGG s+ d++ lcl|NCBI__GCF_000020045.1:WP_012402124.1 140 DGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGINIEATVRLARAVKIPVIASGGLSNLGDIE 208 ********************************************************************* PP TIGR00007 206 alkk...lgvkgvivGkAlyegklklk 229 al + g++gvi+G+A+y+g+l++ lcl|NCBI__GCF_000020045.1:WP_012402124.1 209 ALCEvedEGIEGVICGRAIYSGDLDFA 235 998877799**************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (250 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: 8.19 // [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