Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_011386876.1 AMB_RS22930 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= reanno::Smeli:SMc02570 (247 letters) >NCBI__GCF_000009985.1:WP_011386876.1 Length = 239 Score = 331 bits (849), Expect = 7e-96 Identities = 167/240 (69%), Positives = 201/240 (83%), Gaps = 2/240 (0%) Query: 1 MILFPAIDLKDGQCVRLKLGDMEQATVYNPDPAAQARAFEEQGFEWLHVVDLNGAFAGET 60 M LFPAIDLKDG CVRLKLG ME++TV+N DP AQAR F G EW+HVVDLNGAFAG+ Sbjct: 1 MFLFPAIDLKDGACVRLKLGLMEESTVFNTDPGAQARDFAAAGAEWIHVVDLNGAFAGKP 60 Query: 61 VNGAAVDAILKATKNPVQLGGGIRTLEHIENWLSRGLKRVILGTVAVRDPALVIEACRKF 120 VNGAAVD+ILK+ PVQLGGGIR + IE+WL+RG++RVILGTVA+++PALV EAC++F Sbjct: 61 VNGAAVDSILKSVSVPVQLGGGIREMATIEDWLARGIRRVILGTVALKNPALVKEACQRF 120 Query: 121 PGRVAVGIDAKGGKVAVEGWAEASELGVVELARKFEGAGVAAIIYTDIDRDGILTGINWA 180 PGRVAVGIDAKGGKVAVEGWAE S+L V+ELARKFE GVAA+IYTDIDRDG+L G N A Sbjct: 121 PGRVAVGIDAKGGKVAVEGWAETSDLTVLELARKFEDCGVAALIYTDIDRDGVLAGPNVA 180 Query: 181 STLELADAVSIPVIASGGLASMDDIRRMTEPDAQKLEGAISGRALYDGRIDPKEALDLIR 240 +T LADA+SIPVIASGG++S+ D++ + KLEG ISGRA+YDGRID +A+ L++ Sbjct: 181 ATAALADAISIPVIASGGVSSLVDLKALKA--YPKLEGVISGRAIYDGRIDVAQAIALLK 238 Lambda K H 0.319 0.138 0.401 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: 280 Number of extensions: 10 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: 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 (21.7 bits) S2: 46 (22.3 bits)
Align candidate WP_011386876.1 AMB_RS22930 (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.18926.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-81 258.4 0.1 3.6e-81 258.2 0.1 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386876.1 AMB_RS22930 1-(5-phosphoribosyl) Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011386876.1 AMB_RS22930 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 258.2 0.1 3.6e-81 3.6e-81 2 230 .. 4 232 .. 3 233 .. 0.99 Alignments for each domain: == domain 1 score: 258.2 bits; conditional E-value: 3.6e-81 TIGR00007 2 iPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkivee 70 +PaiDlk+G++vrl G ++++tv+++dp ++a++f++ gae++HvVDL+gA++g+++n ++ +i+++ lcl|NCBI__GCF_000009985.1:WP_011386876.1 4 FPAIDLKDGACVRLKLGLMEESTVFNTDPGAQARDFAAAGAEWIHVVDLNGAFAGKPVNGAAVDSILKS 72 8******************************************************************** PP TIGR00007 71 levkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGW 139 ++v+vq+GGGiR+++++e++l+ g++rvi+gt+a++np+lvke+ +++ +++v++Dak+g+vav+GW lcl|NCBI__GCF_000009985.1:WP_011386876.1 73 VSVPVQLGGGIREMATIEDWLARGIRRVILGTVALKNPALVKEACQRFP-GRVAVGIDAKGGKVAVEGW 140 ************************************************9.******************* PP TIGR00007 140 kekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalk 208 +e+s+l+++ela+k+e++g++++i+Tdi++dG l+G+nv +t l+++ +++viasGGvss d+kalk lcl|NCBI__GCF_000009985.1:WP_011386876.1 141 AETSDLTVLELARKFEDCGVAALIYTDIDRDGVLAGPNVAATAALADAISIPVIASGGVSSLVDLKALK 209 ********************************************************************* PP TIGR00007 209 k.lgvkgvivGkAlyegklklke 230 + +++gvi G+A+y+g++++ + lcl|NCBI__GCF_000009985.1:WP_011386876.1 210 AyPKLEGVISGRAIYDGRIDVAQ 232 97789**************9876 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 8.04 // [ok]
This GapMind analysis is from Apr 09 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