Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate Ga0059261_1048 Ga0059261_1048 imidazoleglycerol phosphate synthase, cyclase subunit
Query= BRENDA::Q5NMD6 (255 letters) >FitnessBrowser__Korea:Ga0059261_1048 Length = 255 Score = 392 bits (1006), Expect = e-114 Identities = 191/252 (75%), Positives = 224/252 (88%), Gaps = 1/252 (0%) Query: 1 MTLCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGR 60 MT+ R+IPCLDVA+GRVVKGVNF +L DAGDPVEQA+ YDAAGADELCFLDI+ASHE R Sbjct: 1 MTVRARVIPCLDVANGRVVKGVNFVNLRDAGDPVEQARAYDAAGADELCFLDITASHEAR 60 Query: 61 GTMLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADR 120 GT++DVV RTAEVCFMPLTVGGGVR EDARALLLAGADKVAVNSAAV RPE+V+EIA+R Sbjct: 61 GTIIDVVRRTAEVCFMPLTVGGGVRSAEDARALLLAGADKVAVNSAAVTRPEVVSEIAER 120 Query: 121 FGAQCVVAAIDARRNGD-HWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGT 179 FG+QC+VA++DARR D WEV+THGGR+PTGI+A++HAL+L +LGAGE+LLTSMD+DGT Sbjct: 121 FGSQCIVASVDARRVADGRWEVFTHGGRKPTGIDAVEHALHLAKLGAGELLLTSMDRDGT 180 Query: 180 RDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEA 239 RDGYDL+L R +AD V VPV+ASGGVGNLDH+V G+ GHASA+LAASIFHFG+ S+ A Sbjct: 181 RDGYDLDLIRTIADRVRVPVVASGGVGNLDHLVAGIRDGHASAVLAASIFHFGEASIVGA 240 Query: 240 HEALAKAGLTVR 251 H ALA AG+ VR Sbjct: 241 HAALAAAGIPVR 252 Lambda K H 0.320 0.136 0.400 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: 332 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: 255 Length of database: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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 (21.8 bits) S2: 47 (22.7 bits)
Align candidate Ga0059261_1048 Ga0059261_1048 (imidazoleglycerol phosphate synthase, cyclase subunit)
to HMM TIGR00735 (hisF: imidazoleglycerol phosphate synthase, cyclase subunit)
# 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/TIGR00735.hmm # target sequence database: /tmp/gapView.4094.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00735 [M=254] Accession: TIGR00735 Description: hisF: imidazoleglycerol phosphate synthase, cyclase subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-105 336.1 2.2 7e-105 335.8 2.2 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_1048 Ga0059261_1048 imidazoleglycerol Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_1048 Ga0059261_1048 imidazoleglycerol phosphate synthase, cyclase subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 335.8 2.2 7e-105 7e-105 4 254 .] 5 252 .. 2 252 .. 0.99 Alignments for each domain: == domain 1 score: 335.8 bits; conditional E-value: 7e-105 TIGR00735 4 kriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaek 72 r+ipCLdv +grvvkGv+f nlrdaGdpve a++yd+ Gadel flditas+e r t+++vv+r+ae lcl|FitnessBrowser__Korea:Ga0059261_1048 5 ARVIPCLDVANGRVVKGVNFVNLRDAGDPVEQARAYDAAGADELCFLDITASHEARGTIIDVVRRTAEV 73 79******************************************************************* PP TIGR00735 73 vfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeak 141 f+PltvgGG++s ed++ ll aGadkv++n+aav++pe+++e+a+rfGsq+iv ++da+r+a+ + lcl|FitnessBrowser__Korea:Ga0059261_1048 74 CFMPLTVGGGVRSAEDARALLLAGADKVAVNSAAVTRPEVVSEIAERFGSQCIVASVDARRVAD---GR 139 *************************************************************997...69 PP TIGR00735 142 yevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGk 210 +ev ++gGr+ t++d+ve a + ++lGaGe+lltsmd+dGt++Gydl l+++++++v++Pv+asgG+G+ lcl|FitnessBrowser__Korea:Ga0059261_1048 140 WEVFTHGGRKPTGIDAVEHALHLAKLGAGELLLTSMDRDGTRDGYDLDLIRTIADRVRVPVVASGGVGN 208 ********************************************************************* PP TIGR00735 211 aehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 +hl ++ +g+a a+Laas+fh++e +i + la+ g++vr lcl|FitnessBrowser__Korea:Ga0059261_1048 209 LDHLVAGIRDGHASAVLAASIFHFGEASIVGAHAALAAAGIPVR 252 ******************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (255 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.47 // [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