Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_013012037.1 DACET_RS14095 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= reanno::psRCH2:GFF155 (247 letters) >NCBI__GCF_000025725.1:WP_013012037.1 Length = 238 Score = 223 bits (568), Expect = 3e-63 Identities = 112/239 (46%), Positives = 162/239 (67%), Gaps = 3/239 (1%) Query: 1 MLIIPAIDLKDGACVRLRQGLMDDATVFSDDPVAMAAKWVEAGCRRLHLVDLNGAFEGQP 60 MLIIPAIDL G VRLRQG MDD TV+ D+P+ A K+ + G +RLH+VDL+GA +G+ Sbjct: 1 MLIIPAIDLLGGKAVRLRQGDMDDYTVYYDNPLDAAKKFADMGVKRLHIVDLDGARDGET 60 Query: 61 VNGEVVTAIAKRYPDLPIQIGGGIRTLETIEHYVRAGVSYVIIGTKAVKEPGFVTEACRA 120 N +++ I + + +++GGG+R L +E Y GV Y I+GT VK+P FV A + Sbjct: 61 TNFDLIEQIVSK-AGMDVEVGGGLRKLVRVEGYFNIGVKYCILGTAVVKDPDFVMAAMKK 119 Query: 121 FPGKVIVGLDAKDGFVATDGWAEVSSVQAVDLARRFEADGVSAIVYTDIAKDGMMQGCNV 180 +P ++I+G+DAKDG VAT+GW E S + A ++ + +E +++YTDI +DGM+ G N+ Sbjct: 120 YPHQIILGIDAKDGCVATEGWYEKSELTAAEVIKSYEGYCAESVIYTDIMRDGMLSGINI 179 Query: 181 EATVALANASRIPVIASGGIHNIGDIQKLLDTNTPGIVGAITGRAIYEGTLDVAEAQAL 239 EAT++LA + PVIASGG+ I DI+ L + I+GAITG+A YEG +D+ EA L Sbjct: 180 EATLSLAEEIQYPVIASGGLKGIEDIEAL--SGKKNILGAITGKAFYEGRIDLEEALRL 236 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: 207 Number of extensions: 7 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: 238 Length adjustment: 23 Effective length of query: 224 Effective length of database: 215 Effective search space: 48160 Effective search space used: 48160 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_013012037.1 DACET_RS14095 (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.17588.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-82 260.6 1.1 7.5e-82 260.4 1.1 1.0 1 lcl|NCBI__GCF_000025725.1:WP_013012037.1 DACET_RS14095 1-(5-phosphoribosy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025725.1:WP_013012037.1 DACET_RS14095 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneami # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.4 1.1 7.5e-82 7.5e-82 1 231 [] 3 233 .. 3 233 .. 0.99 Alignments for each domain: == domain 1 score: 260.4 bits; conditional E-value: 7.5e-82 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 iiPaiDl Gk+vrl qGd+d tvy+d+pl+aakkf+++g+++lH+VDLdgA++ge++n+++i++iv+ lcl|NCBI__GCF_000025725.1:WP_013012037.1 3 IIPAIDLLGGKAVRLRQGDMDDYTVYYDNPLDAAKKFADMGVKRLHIVDLDGARDGETTNFDLIEQIVS 71 8******************************************************************** PP TIGR00007 70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkG 138 ++ ++v+vGGG+R+l +ve ++++gv+++i+gta+v++p++v ++k++ ++i++++Dak+g va++G lcl|NCBI__GCF_000025725.1:WP_013012037.1 72 KAGMDVEVGGGLRKLVRVEGYFNIGVKYCILGTAVVKDPDFVMAAMKKYP-HQIILGIDAKDGCVATEG 139 *************************************************9.9***************** PP TIGR00007 139 WkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkal 207 W eksel+++e++k +e + +e++i+Tdi +dG+lsG+n+e+t +l++e + +viasGG + ied++al lcl|NCBI__GCF_000025725.1:WP_013012037.1 140 WYEKSELTAAEVIKSYEGYCAESVIYTDIMRDGMLSGINIEATLSLAEEIQYPVIASGGLKGIEDIEAL 208 ********************************************************************* PP TIGR00007 208 kk.lgvkgvivGkAlyegklklkea 231 ++ g+i GkA+yeg+++l+ea lcl|NCBI__GCF_000025725.1:WP_013012037.1 209 SGkKNILGAITGKAFYEGRIDLEEA 233 97589****************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (238 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: 6.86 // [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