Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate 8502414 DvMF_3120 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq)
Query= reanno::BFirm:BPHYT_RS17685 (250 letters) >FitnessBrowser__Miya:8502414 Length = 243 Score = 225 bits (573), Expect = 7e-64 Identities = 116/238 (48%), Positives = 157/238 (65%), Gaps = 3/238 (1%) Query: 1 MLLIPAIDLKDGQCVRLKQGDMDQATIFSEEPAAMARHWVDRGARRLHLVDLNGAFAGKP 60 M+L PA+D+KDG+CVRL+QG D T+FS++PAAMARHW D+GA+ LH++DL+GAF+G P Sbjct: 1 MILFPAVDIKDGRCVRLRQGRADAETVFSDDPAAMARHWQDQGAKWLHVIDLDGAFSGMP 60 Query: 61 KNEDAIRAIIEEVGGEIPVQLGGGIRDLNTIERYLDDGLSYVIIGTAAVKNPGFLQDACT 120 N + IR I ++ +PVQLGGGIRD T + YLD G+ +IIGT A++ P C Sbjct: 61 ANFELIRRICADLS--VPVQLGGGIRDEATAKAYLDAGVERLIIGTVALEEPDLYARLCA 118 Query: 121 AFGGHIIVGLDAKDGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGIN 180 F G I V LDA+ G++ T GW +G V D+ + G +IYTDI RDGM G+N Sbjct: 119 TFPGRIGVSLDAEGGRLKTKGWVADSGLTVDDVLPRLLAAGTAFVIYTDIDRDGMQTGVN 178 Query: 181 IEATVRLARAVKIPVIASGGLSNLTDIESLCEVE-DEGIEGVICGRAIYSGDLDFAAA 237 + A RLA +PVIA+GG++ L D+ +L + +EG I GRAIY+G LD AA Sbjct: 179 LSALERLAGMCPVPVIAAGGVATLEDVRALYPMTLTSSVEGAITGRAIYTGTLDLHAA 236 Lambda K H 0.319 0.140 0.410 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: 12 Number of successful extensions: 3 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: 250 Length of database: 243 Length adjustment: 24 Effective length of query: 226 Effective length of database: 219 Effective search space: 49494 Effective search space used: 49494 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 8502414 DvMF_3120 (1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq))
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.2486.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-78 248.7 0.0 3.2e-78 248.5 0.0 1.0 1 lcl|FitnessBrowser__Miya:8502414 DvMF_3120 1-(5-phosphoribosyl)-5 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8502414 DvMF_3120 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazo # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 248.5 0.0 3.2e-78 3.2e-78 2 230 .. 4 235 .. 3 236 .. 0.98 Alignments for each domain: == domain 1 score: 248.5 bits; conditional E-value: 3.2e-78 TIGR00007 2 iPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelevkvqvG 78 +Pa+D+k+G++vrl qG+ d +tv+sddp+++a++++++ga++lHv+DLdgA++g + n+e+i++i+ +l+v+vq+G lcl|FitnessBrowser__Miya:8502414 4 FPAVDIKDGRCVRLRQGRADAETVFSDDPAAMARHWQDQGAKWLHVIDLDGAFSGMPANFELIRRICADLSVPVQLG 80 8**************************************************************************** PP TIGR00007 79 GGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkekselslvelakkle 155 GGiR+ ++++++l++gver+iigt+a+e+p+l ++l +++ +i vslDa++g++++kGW ++s l++ +++ +l lcl|FitnessBrowser__Miya:8502414 81 GGIRDEATAKAYLDAGVERLIIGTVALEEPDLYARLCATFP-GRIGVSLDAEGGRLKTKGWVADSGLTVDDVLPRLL 156 ****************************************9.*********************************** PP TIGR00007 156 elgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalkk....lgvkgvivGkAlyegklkl 228 +g++ +i+Tdi++dG+ +Gvn++++++l+ v+via+GGv++ edv+al+ + v+g+i G+A+y+g+l+l lcl|FitnessBrowser__Miya:8502414 157 AAGTAFVIYTDIDRDGMQTGVNLSALERLAGMCPVPVIAAGGVATLEDVRALYPmtltSSVEGAITGRAIYTGTLDL 233 ****************************************************987777889**************98 PP TIGR00007 229 ke 230 ++ lcl|FitnessBrowser__Miya:8502414 234 HA 235 76 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (243 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: 7.40 // [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