Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_011649868.1 RL_RS00215 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= reanno::Smeli:SMc02570 (247 letters) >NCBI__GCF_000009265.1:WP_011649868.1 Length = 248 Score = 426 bits (1095), Expect = e-124 Identities = 214/243 (88%), Positives = 229/243 (94%) Query: 1 MILFPAIDLKDGQCVRLKLGDMEQATVYNPDPAAQARAFEEQGFEWLHVVDLNGAFAGET 60 MILFPAIDLK GQCVRLKLGDM+QATVYN DPAAQAR+FE+QGFEWLHVVDL+GAFAG + Sbjct: 1 MILFPAIDLKGGQCVRLKLGDMQQATVYNTDPAAQARSFEDQGFEWLHVVDLDGAFAGHS 60 Query: 61 VNGAAVDAILKATKNPVQLGGGIRTLEHIENWLSRGLKRVILGTVAVRDPALVIEACRKF 120 NG AV+AILKAT NPVQLGGGIRTL+HIE WLSRGL+RVILGTVAVR+P LVIEACRKF Sbjct: 61 ANGDAVEAILKATDNPVQLGGGIRTLDHIEAWLSRGLRRVILGTVAVRNPDLVIEACRKF 120 Query: 121 PGRVAVGIDAKGGKVAVEGWAEASELGVVELARKFEGAGVAAIIYTDIDRDGILTGINWA 180 P VAVGIDAKGGKVAVEGWAEASELG++ELARKFEGAGVAAIIYTDIDRDGIL GINW+ Sbjct: 121 PDHVAVGIDAKGGKVAVEGWAEASELGIIELARKFEGAGVAAIIYTDIDRDGILAGINWS 180 Query: 181 STLELADAVSIPVIASGGLASMDDIRRMTEPDAQKLEGAISGRALYDGRIDPKEALDLIR 240 STLELADAVSIPVIASGGLAS+DDIRRM EPDA+KLEGAISGRALYDGRIDPKEAL LI+ Sbjct: 181 STLELADAVSIPVIASGGLASLDDIRRMLEPDARKLEGAISGRALYDGRIDPKEALALIK 240 Query: 241 EAR 243 AR Sbjct: 241 AAR 243 Lambda K H 0.319 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: 356 Number of extensions: 13 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: 247 Length of database: 248 Length adjustment: 24 Effective length of query: 223 Effective length of database: 224 Effective search space: 49952 Effective search space used: 49952 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_011649868.1 RL_RS00215 (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.14583.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-82 260.4 0.0 8.8e-82 260.2 0.0 1.0 1 lcl|NCBI__GCF_000009265.1:WP_011649868.1 RL_RS00215 1-(5-phosphoribosyl)- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009265.1:WP_011649868.1 RL_RS00215 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.2 0.0 8.8e-82 8.8e-82 2 231 .] 4 235 .. 3 235 .. 0.98 Alignments for each domain: == domain 1 score: 260.2 bits; conditional E-value: 8.8e-82 TIGR00007 2 iPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkivee 70 +PaiDlk G++vrl Gd+++ tvy++dp+++a++fe++g+e+lHvVDLdgA++g+ n ++++ i+++ lcl|NCBI__GCF_000009265.1:WP_011649868.1 4 FPAIDLKGGQCVRLKLGDMQQATVYNTDPAAQARSFEDQGFEWLHVVDLDGAFAGHSANGDAVEAILKA 72 8******************************************************************** PP TIGR00007 71 levkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGW 139 ++ +vq+GGGiR+l+++e++l+ g++rvi+gt+av+np+lv e+ +++ ++++v++Dak+g+vav+GW lcl|NCBI__GCF_000009265.1:WP_011649868.1 73 TDNPVQLGGGIRTLDHIEAWLSRGLRRVILGTVAVRNPDLVIEACRKFP-DHVAVGIDAKGGKVAVEGW 140 ************************************************9.99***************** PP TIGR00007 140 kekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalk 208 +e sel ++ela+k+e +g+++ii+Tdi++dG l+G+n + t el+++++++viasGG +s +d++++ lcl|NCBI__GCF_000009265.1:WP_011649868.1 141 AEASELGIIELARKFEGAGVAAIIYTDIDRDGILAGINWSSTLELADAVSIPVIASGGLASLDDIRRML 209 *******************************************************************99 PP TIGR00007 209 k...lgvkgvivGkAlyegklklkea 231 + +++g+i G+Aly+g+++ kea lcl|NCBI__GCF_000009265.1:WP_011649868.1 210 EpdaRKLEGAISGRALYDGRIDPKEA 235 87778899*************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (248 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: 6.99 // [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