Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate 206472 DVU1038 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
Query= reanno::Smeli:SMc02570 (247 letters) >MicrobesOnline__882:206472 Length = 249 Score = 230 bits (587), Expect = 2e-65 Identities = 115/247 (46%), Positives = 167/247 (67%), Gaps = 1/247 (0%) Query: 1 MILFPAIDLKDGQCVRLKLGDMEQATVYNPDPAAQARAFEEQGFEWLHVVDLNGAFAGET 60 MI+FPAIDL +G CVRL+ G + TV++ DP A AR ++EQG WLHVVDL+GAF+G+ Sbjct: 1 MIVFPAIDLMNGVCVRLRRGRADDETVFSSDPVATARHWQEQGGRWLHVVDLDGAFSGQP 60 Query: 61 VNGAAVDAILKATKNPVQLGGGIRTLEHIENWLSRGLKRVILGTVAVRDPALVIEACRKF 120 VN + +I A PVQLGGGIR + +L G++R+I+GT+A+ +P C +F Sbjct: 61 VNAPLIRSICDALDIPVQLGGGIRDAATAKAYLEAGVERLIIGTIALEEPDAYAALCAEF 120 Query: 121 PGRVAVGIDAKGGKVAVEGWAEASELGVVELARKFEGAGVAAIIYTDIDRDGILTGINWA 180 PGR+ V +DA+GGK+ +GW S L V E+ + AG A IIYTDIDRDG+ TG+N Sbjct: 121 PGRIGVSLDAEGGKLKTKGWVADSGLTVDEVLPRLLEAGTAFIIYTDIDRDGMQTGVNLP 180 Query: 181 STLELADAVSIPVIASGGLASMDDIRRMTE-PDAQKLEGAISGRALYDGRIDPKEALDLI 239 + LA A ++PVIA+GG+A+++D++ + L+GA+SGRA+Y+G +D + A+D I Sbjct: 181 ALEHLAKASTVPVIAAGGVATLEDVKALYPLSRTTNLQGAVSGRAIYEGTLDLRTAMDWI 240 Query: 240 REARKGK 246 R+ K + Sbjct: 241 RQQEKAE 247 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: 249 Number of extensions: 8 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: 249 Length adjustment: 24 Effective length of query: 223 Effective length of database: 225 Effective search space: 50175 Effective search space used: 50175 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 206472 DVU1038 (phosphoribosylformimino-5-aminoimidazole carboxamide ribotide 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.31399.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-78 249.2 0.0 2.3e-78 249.0 0.0 1.0 1 lcl|MicrobesOnline__882:206472 DVU1038 phosphoribosylformimino- Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:206472 DVU1038 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 249.0 0.0 2.3e-78 2.3e-78 1 230 [. 3 235 .. 3 236 .. 0.98 Alignments for each domain: == domain 1 score: 249.0 bits; conditional E-value: 2.3e-78 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelevkvqvGG 79 ++PaiDl++G +vrl +G+ d +tv+s dp+++a++++e+g ++lHvVDLdgA++g+++n+++i++i+++l+++vq+GG lcl|MicrobesOnline__882:206472 3 VFPAIDLMNGVCVRLRRGRADDETVFSSDPVATARHWQEQGGRWLHVVDLDGAFSGQPVNAPLIRSICDALDIPVQLGG 81 79***************************************************************************** PP TIGR00007 80 GiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkekselslvelakkleelg 158 GiR++++++++le+gver+iigt+a+e+p+ + l +e+ +i vslDa++g++++kGW ++s l++ e++ +l e+g lcl|MicrobesOnline__882:206472 82 GIRDAATAKAYLEAGVERLIIGTIALEEPDAYAALCAEFP-GRIGVSLDAEGGKLKTKGWVADSGLTVDEVLPRLLEAG 159 ***************************************9.************************************** PP TIGR00007 159 leeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalkk....lgvkgvivGkAlyegklklke 230 ++ ii+Tdi++dG+ +Gvn+ ++++l+k+++v+via+GGv++ edvkal+ ++++g++ G+A+yeg+l+l++ lcl|MicrobesOnline__882:206472 160 TAFIIYTDIDRDGMQTGVNLPALEHLAKASTVPVIAAGGVATLEDVKALYPlsrtTNLQGAVSGRAIYEGTLDLRT 235 *************************************************8777779****************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (249 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: 6.41 // [ok]
This GapMind analysis is from Apr 09 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