Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_013452049.1 CALNI_RS09815 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= reanno::psRCH2:GFF155 (247 letters) >NCBI__GCF_000183405.1:WP_013452049.1 Length = 236 Score = 216 bits (550), Expect = 3e-61 Identities = 110/233 (47%), Positives = 160/233 (68%), Gaps = 4/233 (1%) Query: 1 MLIIPAIDLKDGACVRLRQGLMDDATVFSDDPVAMAAKWVEAGCRRLHLVDLNGAFEGQP 60 ML+IPAIDL G VRL +G MD V+S++P+ +A ++ + G +R+H+VDL+GA +G+ Sbjct: 1 MLLIPAIDLLGGKVVRLEKGDMDKFKVYSENPLDVAKQFEDMGIKRVHIVDLDGAKKGEA 60 Query: 61 VNGEVVTAIAKRYPDLPIQIGGGIRTLETIEHYVRAGVSYVIIGTKAVKEPGFVTEACRA 120 VN ++ I R+ L + +GGGIR ++ E Y GV Y+++GT VK+ F EA + Sbjct: 61 VNYTIIENIV-RHTSLSVDVGGGIRNMKRCEDYFNLGVDYIVLGTAVVKDVDFTKEALQK 119 Query: 121 FPGKVIVGLDAKDGFVATDGWAEVSSVQAVDLARRFEADGVSAIVYTDIAKDGMMQGCNV 180 +P +VI+GLDA+DG++ATDGW E SS+ A+D+ ++ GV+AI+YTDI++DGM+ G NV Sbjct: 120 YPERVILGLDARDGYIATDGWYEKSSLTAIDVIDSYQTYGVAAIIYTDISRDGMLAGINV 179 Query: 181 EATVALANASRIPVIASGGIHNIGDIQKLLDTNTPGIVGAITGRAIYEGTLDV 233 +ATV LAN S PVIASGG+ DI +L N I G I G+A YEG +D+ Sbjct: 180 KATVDLANRSPFPVIASGGLKGEEDIWELKRYN---IFGCIIGKAFYEGKIDL 229 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: 195 Number of extensions: 6 Number of successful extensions: 4 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: 236 Length adjustment: 23 Effective length of query: 224 Effective length of database: 213 Effective search space: 47712 Effective search space used: 47712 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_013452049.1 CALNI_RS09815 (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.11966.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-83 265.7 1.0 2e-83 265.6 1.0 1.0 1 lcl|NCBI__GCF_000183405.1:WP_013452049.1 CALNI_RS09815 1-(5-phosphoribosy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183405.1:WP_013452049.1 CALNI_RS09815 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneami # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 265.6 1.0 2e-83 2e-83 1 230 [. 3 231 .. 3 232 .. 0.99 Alignments for each domain: == domain 1 score: 265.6 bits; conditional E-value: 2e-83 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 +iPaiDl Gkvvrl +Gd+dk +vys++pl++ak+fe++g++++H+VDLdgAk+ge++n ++i++iv+ lcl|NCBI__GCF_000183405.1:WP_013452049.1 3 LIPAIDLLGGKVVRLEKGDMDKFKVYSENPLDVAKQFEDMGIKRVHIVDLDGAKKGEAVNYTIIENIVR 71 59******************************************************************* PP TIGR00007 70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkG 138 +++++v+vGGGiR++++ e++++lgv+++++gta+v++ ++ ke+l+++ e+++++lDa++g +a+ G lcl|NCBI__GCF_000183405.1:WP_013452049.1 72 HTSLSVDVGGGIRNMKRCEDYFNLGVDYIVLGTAVVKDVDFTKEALQKYP-ERVILGLDARDGYIATDG 139 *************************************************9.****************** PP TIGR00007 139 WkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkal 207 W eks+l++++++ ++++g+++ii+Tdi++dG+l+G+nv++t +l++++ +viasGG + +ed+ +l lcl|NCBI__GCF_000183405.1:WP_013452049.1 140 WYEKSSLTAIDVIDSYQTYGVAAIIYTDISRDGMLAGINVKATVDLANRSPFPVIASGGLKGEEDIWEL 208 ********************************************************************* PP TIGR00007 208 kklgvkgvivGkAlyegklklke 230 k+ ++ g i+GkA+yegk++lk+ lcl|NCBI__GCF_000183405.1:WP_013452049.1 209 KRYNIFGCIIGKAFYEGKIDLKT 231 *******************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (236 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: 6.29 // [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