Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate GFF911 PGA1_c09270 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase HisA
Query= reanno::Smeli:SMc02570 (247 letters) >FitnessBrowser__Phaeo:GFF911 Length = 240 Score = 288 bits (737), Expect = 7e-83 Identities = 152/240 (63%), Positives = 183/240 (76%), Gaps = 1/240 (0%) Query: 1 MILFPAIDLKDGQCVRLKLGDMEQATVYNPDPAAQARAFEEQGFEWLHVVDLNGAFAGET 60 MIL+PAIDLKDGQ VRL GDME+ TV+N DPAAQA F E G +WLH+VDLNGAFAGE Sbjct: 1 MILYPAIDLKDGQAVRLLHGDMEKTTVFNDDPAAQALEFVEAGCDWLHLVDLNGAFAGEP 60 Query: 61 VNGAAVDAILKATKNPVQLGGGIRTLEHIENWLSRGLKRVILGTVAVRDPALVIEACRKF 120 VN A V+ ILK K P QLGGGIR + IE W+ +GL RVILGTVAV +P LV EA R F Sbjct: 61 VNAAPVEKILKRCKVPAQLGGGIRDMATIERWIDKGLARVILGTVAVENPDLVREAARAF 120 Query: 121 PGRVAVGIDAKGGKVAVEGWAEASELGVVELARKFEGAGVAAIIYTDIDRDGILTGINWA 180 PG+VAVGIDA+ G+VA +GWAE +++ V +LA+ FE AGVAAIIYTDI RDG + G N Sbjct: 121 PGKVAVGIDARNGRVATKGWAEETDVMVTDLAKSFEDAGVAAIIYTDILRDGAMKGPNVE 180 Query: 181 STLELADAVSIPVIASGGLASMDDIRRMTEPDAQKLEGAISGRALYDGRIDPKEALDLIR 240 +T LA+AVSIPVIASGG++S+ D++ + A L GAISGRALYDG ID EAL +++ Sbjct: 181 ATAALANAVSIPVIASGGVSSLADLQALKSCGA-PLNGAISGRALYDGAIDLGEALKILK 239 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: 257 Number of extensions: 9 Number of successful extensions: 2 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: 240 Length adjustment: 23 Effective length of query: 224 Effective length of database: 217 Effective search space: 48608 Effective search space used: 48608 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 GFF911 PGA1_c09270 (1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase HisA)
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.32419.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-83 265.4 0.0 2.6e-83 265.2 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF911 PGA1_c09270 1-(5-phosphoribosyl) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF911 PGA1_c09270 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imida # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 265.2 0.0 2.6e-83 2.6e-83 1 230 [. 3 233 .. 3 234 .. 0.98 Alignments for each domain: == domain 1 score: 265.2 bits; conditional E-value: 2.6e-83 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelevkvqv 77 ++PaiDlk+G++vrl++Gd++k+tv++ddp+++a +f e g ++lH+VDL+gA++ge++n+ ++ki+++++v+ q+ lcl|FitnessBrowser__Phaeo:GFF911 3 LYPAIDLKDGQAVRLLHGDMEKTTVFNDDPAAQALEFVEAGCDWLHLVDLNGAFAGEPVNAAPVEKILKRCKVPAQL 79 59*************************************************************************** PP TIGR00007 78 GGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkekselslvelakkl 154 GGGiR+++++e+++++g++rvi+gt+avenp+lv+e+++++ k++v++Da++g+va+kGW+e++++ +++lak + lcl|FitnessBrowser__Phaeo:GFF911 80 GGGIRDMATIERWIDKGLARVILGTVAVENPDLVREAARAFP-GKVAVGIDARNGRVATKGWAEETDVMVTDLAKSF 155 *****************************************9.9********************************* PP TIGR00007 155 eelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalkk..lgvkgvivGkAlyegklklk 229 e++g+++ii+Tdi +dG ++G+nve+t l+++++++viasGGvss +d++alk+ + ++g+i G+Aly+g ++l lcl|FitnessBrowser__Phaeo:GFF911 156 EDAGVAAIIYTDILRDGAMKGPNVEATAALANAVSIPVIASGGVSSLADLQALKScgAPLNGAISGRALYDGAIDLG 232 *******************************************************545579*************987 PP TIGR00007 230 e 230 e lcl|FitnessBrowser__Phaeo:GFF911 233 E 233 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (240 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: 9.72 // [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