Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate Synpcc7942_1829 Synpcc7942_1829 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= reanno::BFirm:BPHYT_RS17685 (250 letters) >FitnessBrowser__SynE:Synpcc7942_1829 Length = 256 Score = 230 bits (587), Expect = 2e-65 Identities = 119/237 (50%), Positives = 159/237 (67%), Gaps = 2/237 (0%) Query: 1 MLLIPAIDLKDGQCVRLKQGDMDQATIFSEEPAAMARHWVDRGARRLHLVDLNGAFAGKP 60 M +IPAIDL GQCVRL QGD DQA ++ ++P MA W + GA+RLHLVDL+GA G P Sbjct: 1 MDVIPAIDLLGGQCVRLFQGDYDQAEVYGKDPVGMALRWAEAGAQRLHLVDLDGAKEGSP 60 Query: 61 KNEDAIRAIIEEVGGEIPVQLGGGIRDLNTIERYLDDGLSYVIIGTAAVKNPGFLQDACT 120 N +AI I + + IPVQ+GGG+RD +T+ R LD G+ I+GT AV+ P ++ Sbjct: 61 VNAEAIATIAQRLS--IPVQVGGGLRDRDTVARLLDSGVERAILGTVAVERPALVEALAG 118 Query: 121 AFGGHIIVGLDAKDGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGIN 180 F G I VG+DA+ GKVAT GW + +G LA++ D G ++I TDIGRDG LQG N Sbjct: 119 EFPGQIAVGIDARSGKVATRGWLEDSGLTAVALAQQMADLGACALICTDIGRDGTLQGPN 178 Query: 181 IEATVRLARAVKIPVIASGGLSNLTDIESLCEVEDEGIEGVICGRAIYSGDLDFAAA 237 +E +A AV IPVIASGG+ +LTD+ SL +E +G+ GVI G+A+Y+G +D A Sbjct: 179 LEELRAIAAAVSIPVIASGGVGSLTDLLSLLPLEAQGVSGVIVGKALYTGAVDLQEA 235 Score = 33.9 bits (76), Expect = 3e-06 Identities = 30/93 (32%), Positives = 41/93 (44%), Gaps = 5/93 (5%) Query: 34 AMARHWVDRGARRLHLVDLNGAFAGKPKNEDAIRAIIEEVGGEIPVQLGGGIRDLNTIER 93 A+A+ D GA L D+ + N + +RAI V IPV GG+ L + Sbjct: 150 ALAQQMADLGACALICTDIGRDGTLQGPNLEELRAIAAAVS--IPVIASGGVGSLTDLLS 207 Query: 94 YLD---DGLSYVIIGTAAVKNPGFLQDACTAFG 123 L G+S VI+G A LQ+A A G Sbjct: 208 LLPLEAQGVSGVIVGKALYTGAVDLQEALRAIG 240 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: 246 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 250 Length of database: 256 Length adjustment: 24 Effective length of query: 226 Effective length of database: 232 Effective search space: 52432 Effective search space used: 52432 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 Synpcc7942_1829 Synpcc7942_1829 (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.24802.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-84 268.7 0.1 2.4e-84 268.6 0.1 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1829 Synpcc7942_1829 1-(5-phosphoribo Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1829 Synpcc7942_1829 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylidene # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 268.6 0.1 2.4e-84 2.4e-84 1 231 [] 3 235 .. 3 235 .. 0.97 Alignments for each domain: == domain 1 score: 268.6 bits; conditional E-value: 2.4e-84 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 +iPaiDl G++vrl+qGd+d+ +vy++dp+ +a +++e ga++lH+VDLdgAkeg+++n+e+i++i++ lcl|FitnessBrowser__SynE:Synpcc7942_1829 3 VIPAIDLLGGQCVRLFQGDYDQAEVYGKDPVGMALRWAEAGAQRLHLVDLDGAKEGSPVNAEAIATIAQ 71 89******************************************************************* PP TIGR00007 70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkG 138 +l+++vqvGGG+R++++v++ll+ gver i+gt+ave+p+lv+ l+ e+ +i+v++Da++g+va++G lcl|FitnessBrowser__SynE:Synpcc7942_1829 72 RLSIPVQVGGGLRDRDTVARLLDSGVERAILGTVAVERPALVEALAGEFP-GQIAVGIDARSGKVATRG 139 *************************************************9.99**************** PP TIGR00007 139 WkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkal 207 W e+s l++v la+++++lg+ ++i+Tdi +dGtl+G+n+e ++ ++++++++viasGGv s +d+ +l lcl|FitnessBrowser__SynE:Synpcc7942_1829 140 WLEDSGLTAVALAQQMADLGACALICTDIGRDGTLQGPNLEELRAIAAAVSIPVIASGGVGSLTDLLSL 208 *****************************************************************9886 PP TIGR00007 208 kk...lgvkgvivGkAlyegklklkea 231 +gv+gvivGkAly+g ++l+ea lcl|FitnessBrowser__SynE:Synpcc7942_1829 209 LPleaQGVSGVIVGKALYTGAVDLQEA 235 4433399***************99985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (256 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: 7.04 // [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