Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_012101686.1 CKL_RS06395 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= reanno::Caulo:CCNA_03852 (244 letters) >NCBI__GCF_000016505.1:WP_012101686.1 Length = 238 Score = 207 bits (526), Expect = 2e-58 Identities = 105/236 (44%), Positives = 156/236 (66%), Gaps = 3/236 (1%) Query: 4 MILYPAIDLKDGQCVRLLHGDMDKATVFNTSPADQAQRFVQDGFSWLHVVDLNGAIEGKS 63 MI+ PAIDLK G+CVRL GDM+ V P + A +F +G +LH+VDL+GA++G Sbjct: 1 MIILPAIDLKGGKCVRLYKGDMNSQEVVARDPFETALKFKSEGAQYLHMVDLDGALKGSG 60 Query: 64 VNTAAVEQILESISIPVQLGGGIRTLEGVEAWIEAGVSRVILGTVAVHDPELVKKAARLW 123 N + +I++++ +P+++GGGIR +E ++ +I+ GVSRVILGT A+ + ELV KA + Sbjct: 61 ENLDIISKIVKNVDVPIEVGGGIRNIETIDKFIKLGVSRVILGTAALKNKELVIKAVENY 120 Query: 124 PEQIAVAVDVRDGKVAVDGWTGLSDLSAIDLSRRFEDAGVAALIITDISRDGALTGVNVE 183 E+IAV +D +DG A DGWT LS + ID + E GV LI TDIS+DG L G N+E Sbjct: 121 DEKIAVGIDAKDGVPAADGWTTLSKTNYIDFGKEMEKIGVQTLIFTDISKDGTLEGTNLE 180 Query: 184 GVGELADAVSIPVIASGGVAAVADIERLKARQGVEIAGAILGRSLYAGTIKPSEAL 239 + +L ++V VIASGG+ + DI+ LK + GAI+G+++YA T+ +A+ Sbjct: 181 QLLKLKNSVKCNVIASGGIKDIEDIKSLKKE---NVYGAIVGKAIYAKTLSLKKAI 233 Score = 26.2 bits (56), Expect = 6e-04 Identities = 29/115 (25%), Positives = 49/115 (42%), Gaps = 9/115 (7%) Query: 10 IDLKDGQCVRLLHGDMDKATVFNTSPADQAQRFVQDGFSWLHVVDLN--GAIEGKSVNTA 67 ID KDG V G T+ T+ D + + G L D++ G +EG N Sbjct: 128 IDAKDG--VPAADG---WTTLSKTNYIDFGKEMEKIGVQTLIFTDISKDGTLEG--TNLE 180 Query: 68 AVEQILESISIPVQLGGGIRTLEGVEAWIEAGVSRVILGTVAVHDPELVKKAARL 122 + ++ S+ V GGI+ +E +++ + V I+G +KKA + Sbjct: 181 QLLKLKNSVKCNVIASGGIKDIEDIKSLKKENVYGAIVGKAIYAKTLSLKKAIEI 235 Lambda K H 0.318 0.135 0.384 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: 188 Number of extensions: 8 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 244 Length of database: 238 Length adjustment: 23 Effective length of query: 221 Effective length of database: 215 Effective search space: 47515 Effective search space used: 47515 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
Align candidate WP_012101686.1 CKL_RS06395 (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.3055.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-87 277.8 5.2 4.2e-87 277.6 5.2 1.0 1 lcl|NCBI__GCF_000016505.1:WP_012101686.1 CKL_RS06395 1-(5-phosphoribosyl) Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016505.1:WP_012101686.1 CKL_RS06395 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 277.6 5.2 4.2e-87 4.2e-87 1 230 [. 3 231 .. 3 232 .. 0.99 Alignments for each domain: == domain 1 score: 277.6 bits; conditional E-value: 4.2e-87 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 i+PaiDlk Gk+vrl++Gd+++++v+++dp e+a kf++ega++lH+VDLdgA +g+ +nl++i+kiv+ lcl|NCBI__GCF_000016505.1:WP_012101686.1 3 ILPAIDLKGGKCVRLYKGDMNSQEVVARDPFETALKFKSEGAQYLHMVDLDGALKGSGENLDIISKIVK 71 89******************************************************************* PP TIGR00007 70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkG 138 +++v+++vGGGiR++e+++k+++lgv+rvi+gtaa++n+elv +++++++ eki+v++Dak+g a G lcl|NCBI__GCF_000016505.1:WP_012101686.1 72 NVDVPIEVGGGIRNIETIDKFIKLGVSRVILGTAALKNKELVIKAVENYD-EKIAVGIDAKDGVPAADG 139 *************************************************9.****************** PP TIGR00007 139 WkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkal 207 W+ s+ +++++ k++e++g++++i+Tdi+kdGtl+G+n+e++ +l+++++++viasGG+++ied+k+l lcl|NCBI__GCF_000016505.1:WP_012101686.1 140 WTTLSKTNYIDFGKEMEKIGVQTLIFTDISKDGTLEGTNLEQLLKLKNSVKCNVIASGGIKDIEDIKSL 208 ********************************************************************* PP TIGR00007 208 kklgvkgvivGkAlyegklklke 230 kk +v+g+ivGkA+y ++l+lk+ lcl|NCBI__GCF_000016505.1:WP_012101686.1 209 KKENVYGAIVGKAIYAKTLSLKK 231 *******************9987 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: 6.74 // [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