Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_009543780.1 CCE_RS19555 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= reanno::azobra:AZOBR_RS01680 (249 letters) >NCBI__GCF_000017845.1:WP_009543780.1 Length = 257 Score = 240 bits (613), Expect = 2e-68 Identities = 122/241 (50%), Positives = 165/241 (68%) Query: 1 MIIYPAIDLKDGACVRLLRGEMSQATVFNTEPADQARLFESQGFEWLHLVDLNGAFEGKP 60 M + PAIDL +G CVRL +G Q+ V+N P + AR + +G LHLVDL+GA +G P Sbjct: 1 MDVIPAIDLLEGRCVRLYQGNYQQSEVYNENPVEVARQWADEGATRLHLVDLDGAKQGHP 60 Query: 61 VNGKAVESILGAVAIPVQLGGGIRDLKTIAHWLEKGVSRVILGTVALREPELVREACREF 120 VN +E+I+ A++IPVQ+GGG+RD ++IA ++ GV R I+GTVA+ P LV+E C+ F Sbjct: 61 VNLDTIEAIVRAISIPVQVGGGLRDRQSIAQLIDLGVDRTIVGTVAVENPSLVQELCQAF 120 Query: 121 PGKVAVGIDAREGYVAVAGWAETSTIKALDLALKFEDSGVAAIIYTDINRDGAMGGVNVE 180 P K+AVGIDAR G VA GW ETS + A +LA + + GV+AIIYTDI+RDG + G N E Sbjct: 121 PSKIAVGIDARNGKVATRGWLETSEVLATELAQQMAELGVSAIIYTDIHRDGTLQGPNRE 180 Query: 181 ATSDLAFHLTTPVIASGGVSSIDDLIALKKEEDTGIEGVICGRALYDGRIDPKTALDLLS 240 A +LA H+ PVIASGGVSS+ D++ L E G+ GVI G+ALY G + A+ + Sbjct: 181 ALRELANHIKIPVIASGGVSSLSDVLGLLALEPIGVTGVIIGKALYTGDVSLAEAVHAVG 240 Query: 241 P 241 P Sbjct: 241 P 241 Lambda K H 0.318 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: 233 Number of extensions: 15 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: 249 Length of database: 257 Length adjustment: 24 Effective length of query: 225 Effective length of database: 233 Effective search space: 52425 Effective search space used: 52425 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
Align candidate WP_009543780.1 CCE_RS19555 (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.26091.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-90 288.5 0.4 2.2e-90 288.4 0.4 1.0 1 lcl|NCBI__GCF_000017845.1:WP_009543780.1 CCE_RS19555 1-(5-phosphoribosyl) Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017845.1:WP_009543780.1 CCE_RS19555 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 288.4 0.4 2.2e-90 2.2e-90 1 230 [. 3 234 .. 3 235 .. 0.97 Alignments for each domain: == domain 1 score: 288.4 bits; conditional E-value: 2.2e-90 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 +iPaiDl eG++vrl+qG++++++vy+++p+e+a+++++ega++lH+VDLdgAk+g+++nl++i+ iv+ lcl|NCBI__GCF_000017845.1:WP_009543780.1 3 VIPAIDLLEGRCVRLYQGNYQQSEVYNENPVEVARQWADEGATRLHLVDLDGAKQGHPVNLDTIEAIVR 71 89******************************************************************* PP TIGR00007 70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkG 138 +++++vqvGGG+R+++++++l++lgv+r i+gt+avenp+lv+el +++ +ki+v++Da++g+va++G lcl|NCBI__GCF_000017845.1:WP_009543780.1 72 AISIPVQVGGGLRDRQSIAQLIDLGVDRTIVGTVAVENPSLVQELCQAFP-SKIAVGIDARNGKVATRG 139 *************************************************9.99**************** PP TIGR00007 139 WkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkal 207 W e+se+ ++ela++++elg+++ii+Tdi++dGtl+G+n e+++el+++ +++viasGGvss +dv l lcl|NCBI__GCF_000017845.1:WP_009543780.1 140 WLETSEVLATELAQQMAELGVSAIIYTDIHRDGTLQGPNREALRELANHIKIPVIASGGVSSLSDVLGL 208 *****************************************************************9765 PP TIGR00007 208 kk...lgvkgvivGkAlyegklklke 230 + +gv+gvi+GkAly+g+++l e lcl|NCBI__GCF_000017845.1:WP_009543780.1 209 LAlepIGVTGVIIGKALYTGDVSLAE 234 554459***************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (257 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: 10.63 // [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