Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_078715612.1 B5D49_RS00040 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= reanno::Putida:PP_0292 (245 letters) >NCBI__GCF_900167125.1:WP_078715612.1 Length = 243 Score = 251 bits (641), Expect = 9e-72 Identities = 124/244 (50%), Positives = 167/244 (68%), Gaps = 1/244 (0%) Query: 1 MLIIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQP 60 M++ PA+D+KDG CVRL QG+ + TVFS DPV+MA +W + GC LH++DL+GAF GQP Sbjct: 1 MILFPAVDIKDGQCVRLSQGKEDQVTVFSPDPVAMAQQWADRGCEYLHVIDLDGAFSGQP 60 Query: 61 VNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKQPEFVAEACKA 120 N E++ I ++P+Q+GGG+R L + Y+ AGV +IIGT A++QPE AE C A Sbjct: 61 RNAELIRRICTAI-DIPVQLGGGVRDLTIAKAYLDAGVQRLIIGTLALEQPERFAELCSA 119 Query: 121 FPGKVIVGLDAKDGFVATDGWAEVSSVQVIDLAKRFEADGVSAIVYTDIAKDGMMQGCNV 180 FPG+V V LDA DG + T GW E + + D+ + E G + I+YTDIA+DGM G N+ Sbjct: 120 FPGQVGVSLDAVDGMLKTKGWVEDAGQHIFDVLPQMEKAGAAFIIYTDIARDGMQTGVNL 179 Query: 181 PFTKALAEATRIPVIASGGIHNLGDIKALLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC 240 +AL E T IPVIA+GG+H L D+KAL A G+ GAI+GRAIY GTLDV+ AQ + Sbjct: 180 EALEALCEKTTIPVIAAGGVHTLDDLKALYPLCAKGLEGAISGRAIYTGTLDVSAAQDWI 239 Query: 241 DNYQ 244 + Q Sbjct: 240 RSMQ 243 Lambda K H 0.320 0.138 0.408 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: 228 Number of extensions: 6 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: 245 Length of database: 243 Length adjustment: 24 Effective length of query: 221 Effective length of database: 219 Effective search space: 48399 Effective search space used: 48399 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_078715612.1 B5D49_RS00040 (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.29518.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-78 249.6 0.0 1.7e-78 249.4 0.0 1.0 1 lcl|NCBI__GCF_900167125.1:WP_078715612.1 B5D49_RS00040 1-(5-phosphoribosy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900167125.1:WP_078715612.1 B5D49_RS00040 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneami # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 249.4 0.0 1.7e-78 1.7e-78 2 230 .. 4 234 .. 3 235 .. 0.98 Alignments for each domain: == domain 1 score: 249.4 bits; conditional E-value: 1.7e-78 TIGR00007 2 iPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkivee 70 +Pa+D+k+G++vrl qG++d+ tv+s dp+++a+++++ g e+lHv+DLdgA++g+++n+e+i++i+++ lcl|NCBI__GCF_900167125.1:WP_078715612.1 4 FPAVDIKDGQCVRLSQGKEDQVTVFSPDPVAMAQQWADRGCEYLHVIDLDGAFSGQPRNAELIRRICTA 72 8******************************************************************** PP TIGR00007 71 levkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGW 139 ++++vq+GGG+R+l ++++l++gv+r+iigt+a+e+pe ++el +++ ++ vslDa +g +++kGW lcl|NCBI__GCF_900167125.1:WP_078715612.1 73 IDIPVQLGGGVRDLTIAKAYLDAGVQRLIIGTLALEQPERFAELCSAFP-GQVGVSLDAVDGMLKTKGW 140 ************************************************9.99***************** PP TIGR00007 140 kekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalk 208 e++ ++++++ ++e++g++ ii+Tdi++dG+ +Gvn+e+++ l+++++++via+GGv++ +d+kal+ lcl|NCBI__GCF_900167125.1:WP_078715612.1 141 VEDAGQHIFDVLPQMEKAGAAFIIYTDIARDGMQTGVNLEALEALCEKTTIPVIAAGGVHTLDDLKALY 209 *******************************************************************99 PP TIGR00007 209 k...lgvkgvivGkAlyegklklke 230 g++g+i G+A+y+g+l++++ lcl|NCBI__GCF_900167125.1:WP_078715612.1 210 PlcaKGLEGAISGRAIYTGTLDVSA 234 8777999**************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (243 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: 9.02 // [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