Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_086508672.1 BZY95_RS03885 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= reanno::psRCH2:GFF155 (247 letters) >NCBI__GCF_002151265.1:WP_086508672.1 Length = 250 Score = 380 bits (977), Expect = e-110 Identities = 186/241 (77%), Positives = 209/241 (86%) Query: 1 MLIIPAIDLKDGACVRLRQGLMDDATVFSDDPVAMAAKWVEAGCRRLHLVDLNGAFEGQP 60 ML+IPAIDLKDG CVRL+QG MDDAT + DDPVAMAA+WVEAG RRLHLVDLNGAFEG+P Sbjct: 1 MLVIPAIDLKDGKCVRLKQGRMDDATTYGDDPVAMAARWVEAGARRLHLVDLNGAFEGKP 60 Query: 61 VNGEVVTAIAKRYPDLPIQIGGGIRTLETIEHYVRAGVSYVIIGTKAVKEPGFVTEACRA 120 +NGE VTAIA+R+P+LPIQIGGGIR+ ETIEHY+ AGVSYVIIGTKAVKEP FV E CRA Sbjct: 61 INGEAVTAIARRWPELPIQIGGGIRSAETIEHYLAAGVSYVIIGTKAVKEPAFVGEVCRA 120 Query: 121 FPGKVIVGLDAKDGFVATDGWAEVSSVQAVDLARRFEADGVSAIVYTDIAKDGMMQGCNV 180 FPG VIVGLDA+DGFVATDGWAEVS V+AVDLA+RF DGVS+IVYTDIA+DGMM G NV Sbjct: 121 FPGHVIVGLDARDGFVATDGWAEVSQVKAVDLAKRFADDGVSSIVYTDIARDGMMNGVNV 180 Query: 181 EATVALANASRIPVIASGGIHNIGDIQKLLDTNTPGIVGAITGRAIYEGTLDVAEAQALC 240 EAT LA +PVIASGG+ N+ D++ L+ PGI+GAITGRAIYEGTLDVAE Q LC Sbjct: 181 EATAELAREGGLPVIASGGVTNLDDLRALVAAGEPGILGAITGRAIYEGTLDVAEGQRLC 240 Query: 241 D 241 D Sbjct: 241 D 241 Lambda K H 0.320 0.138 0.405 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: 346 Number of extensions: 8 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: 250 Length adjustment: 24 Effective length of query: 223 Effective length of database: 226 Effective search space: 50398 Effective search space used: 50398 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 (21.8 bits) S2: 46 (22.3 bits)
Align candidate WP_086508672.1 BZY95_RS03885 (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.26986.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-82 260.1 0.5 1e-81 259.9 0.5 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508672.1 BZY95_RS03885 1-(5-phosphoribosy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508672.1 BZY95_RS03885 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneami # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 259.9 0.5 1e-81 1e-81 1 230 [. 3 235 .. 3 236 .. 0.97 Alignments for each domain: == domain 1 score: 259.9 bits; conditional E-value: 1e-81 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 +iPaiDlk+Gk+vrl qG++d t+y+ddp+++a+++ e ga++lH+VDL+gA+eg++ n e++ i++ lcl|NCBI__GCF_002151265.1:WP_086508672.1 3 VIPAIDLKDGKCVRLKQGRMDDATTYGDDPVAMAARWVEAGARRLHLVDLNGAFEGKPINGEAVTAIAR 71 89*****************************************************************99 PP TIGR00007 70 el.evkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavk 137 + e+++q+GGGiRs+e++e++l++gv++viigt+av++p++v e+ +++ +++v+lDa++g va+ lcl|NCBI__GCF_002151265.1:WP_086508672.1 72 RWpELPIQIGGGIRSAETIEHYLAAGVSYVIIGTKAVKEPAFVGEVCRAFP-GHVIVGLDARDGFVATD 139 86489*********************************************9.99*************** PP TIGR00007 138 GWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvka 206 GW+e s++++v+lak++++ g+++i++Tdi++dG+++Gvnve+t el++e +viasGGv++ +d++a lcl|NCBI__GCF_002151265.1:WP_086508672.1 140 GWAEVSQVKAVDLAKRFADDGVSSIVYTDIARDGMMNGVNVEATAELAREGGLPVIASGGVTNLDDLRA 208 ********************************************************************9 PP TIGR00007 207 lkk...lgvkgvivGkAlyegklklke 230 l + g+ g+i G+A+yeg+l++ e lcl|NCBI__GCF_002151265.1:WP_086508672.1 209 LVAagePGILGAITGRAIYEGTLDVAE 235 98845567899************9865 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.49 // [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