Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_055437260.1 ASC41_RS13930 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= reanno::Btheta:350907 (239 letters) >NCBI__GCF_001418085.1:WP_055437260.1 Length = 241 Score = 303 bits (775), Expect = 3e-87 Identities = 142/238 (59%), Positives = 189/238 (79%) Query: 2 IEIIPAIDIIDGKCVRLSQGDYDSKKVYNENPVEVAKEFEANGVRRLHVVDLDGAASHHV 61 + IIPAIDIIDGKCVRLS+GDY++KK+YNE+P+EVAK FE G++ LHVVDLDGA + H+ Sbjct: 1 MRIIPAIDIIDGKCVRLSKGDYNTKKIYNESPLEVAKSFEGAGIQYLHVVDLDGAKAKHI 60 Query: 62 VNHRVLEQIATRTSLIVDFGGGVKSDEDLKIAFESGAQMVTGGSVAVKDPELFCHWLEVY 121 +NH+VLEQIAT+T+L +DFGGG+K++EDLKIAF SGA +TGGS+AVK+P++F WL + Sbjct: 61 INHKVLEQIATKTNLKIDFGGGLKTNEDLKIAFNSGASQITGGSIAVKNPKIFQEWLTKF 120 Query: 122 GSEKIILGADVKEHKIAVNGWKDESACELFPFLEDYINKGIQKVICTDISCDGMLKGPSI 181 GS+KIILGAD IA++GW +ES ++ PF++DY KG VICTDIS DGML+GPS Sbjct: 121 GSDKIILGADCNNENIAISGWLEESDLKVIPFIQDYQTKGASYVICTDISKDGMLEGPSF 180 Query: 182 DLYKEMLEKFPNLYLMASGGVSNVDDIIALNEAGVPGVIFGKALYEGHITLKDLRIFL 239 +LY+ +L++ NL L+ASGG+S D++ L E G GVI GKA+YE I+LK L ++ Sbjct: 181 ELYERILKETKNLNLIASGGISTFDELPKLAELGCEGVIIGKAIYENRISLKQLENYI 238 Lambda K H 0.320 0.140 0.413 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: 229 Number of extensions: 4 Number of successful extensions: 1 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: 239 Length of database: 241 Length adjustment: 23 Effective length of query: 216 Effective length of database: 218 Effective search space: 47088 Effective search space used: 47088 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 (21.7 bits) S2: 46 (22.3 bits)
Align candidate WP_055437260.1 ASC41_RS13930 (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.3741163.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-81 257.2 0.1 8.4e-81 257.0 0.1 1.0 1 NCBI__GCF_001418085.1:WP_055437260.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001418085.1:WP_055437260.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.0 0.1 8.4e-81 8.4e-81 1 230 [. 3 233 .. 3 234 .. 0.99 Alignments for each domain: == domain 1 score: 257.0 bits; conditional E-value: 8.4e-81 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelev 73 iiPaiD+++Gk+vrl +Gd+++k++y+++ple+ak+fe g+++lHvVDLdgAk+++ n +v+++i++++++ NCBI__GCF_001418085.1:WP_055437260.1 3 IIPAIDIIDGKCVRLSKGDYNTKKIYNESPLEVAKSFEGAGIQYLHVVDLDGAKAKHIINHKVLEQIATKTNL 75 8************************************************************************ PP TIGR00007 74 kvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkeksels 146 k++ GGG+++ e+++ +++ g++++ g++av+np++++e+l+++gs+ki+++ D +++++a++GW e+s+l+ NCBI__GCF_001418085.1:WP_055437260.1 76 KIDFGGGLKTNEDLKIAFNSGASQITGGSIAVKNPKIFQEWLTKFGSDKIILGADCNNENIAISGWLEESDLK 148 ************************************************************************* PP TIGR00007 147 lvelakkleelgleeiilTdiekdGtlsGvnveltkelvke.aeveviasGGvssiedvkalkklgvkgvivG 218 ++ +++ +++ g++ +i+Tdi+kdG+l+G+ +el+++++ke ++ ++iasGG+s+ +++ +l++lg++gvi+G NCBI__GCF_001418085.1:WP_055437260.1 149 VIPFIQDYQTKGASYVICTDISKDGMLEGPSFELYERILKEtKNLNLIASGGISTFDELPKLAELGCEGVIIG 221 *****************************************99****************************** PP TIGR00007 219 kAlyegklklke 230 kA+ye++++lk+ NCBI__GCF_001418085.1:WP_055437260.1 222 KAIYENRISLKQ 233 ********9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (241 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 20.40 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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