Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate SMc02569 SMc02569 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q5NMD6 (255 letters) >FitnessBrowser__Smeli:SMc02569 Length = 258 Score = 358 bits (920), Expect = e-104 Identities = 176/256 (68%), Positives = 208/256 (81%), Gaps = 5/256 (1%) Query: 1 MTLCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGR 60 MTL R+IPCLDV DGRVVKGVNF DL+DAGDPVE A+ YDAAGADELCFLDI+AS + R Sbjct: 1 MTLKARVIPCLDVKDGRVVKGVNFVDLIDAGDPVEAARAYDAAGADELCFLDITASSDNR 60 Query: 61 GTMLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADR 120 T+ DVVARTAE CFMPLTVGGGVRQV D R LLLAGADKV++N+AAV PE VAE AD+ Sbjct: 61 ETIFDVVARTAEQCFMPLTVGGGVRQVADIRKLLLAGADKVSINTAAVKNPEFVAEAADK 120 Query: 121 FGAQCVVAAIDARR-----NGDHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMD 175 FG QC+V AIDA++ D WE++THGGR+PTGI+A++ A + LGAGEILLTSMD Sbjct: 121 FGDQCIVVAIDAKKVSAQGEADRWEIFTHGGRQPTGIDAIEFARKVVDLGAGEILLTSMD 180 Query: 176 KDGTRDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYS 235 +DGT+ GYD+ LTR +AD+V PVIASGGVG LDHMVEG+ GHA+A+LAASIFHFG YS Sbjct: 181 RDGTKSGYDISLTRAIADAVRAPVIASGGVGTLDHMVEGIRDGHATAVLAASIFHFGTYS 240 Query: 236 LAEAHEALAKAGLTVR 251 + EA +AK G+ +R Sbjct: 241 IGEAKRHMAKHGIAMR 256 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: 286 Number of extensions: 7 Number of successful extensions: 2 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: 258 Length adjustment: 24 Effective length of query: 231 Effective length of database: 234 Effective search space: 54054 Effective search space used: 54054 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 SMc02569 SMc02569 (imidazole glycerol phosphate synthase subunit HisF)
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.24143.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-111 357.4 4.2 2.1e-111 357.2 4.2 1.0 1 lcl|FitnessBrowser__Smeli:SMc02569 SMc02569 imidazole glycerol phos Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc02569 SMc02569 imidazole glycerol phosphate synthase subunit HisF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 357.2 4.2 2.1e-111 2.1e-111 2 254 .] 3 256 .. 2 256 .. 0.98 Alignments for each domain: == domain 1 score: 357.2 bits; conditional E-value: 2.1e-111 TIGR00735 2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvfiP 76 l r+ipCLdvkdgrvvkGv+f +l daGdpve a++yd+ Gadel flditass++ret+ +vv r+ae+ f+P lcl|FitnessBrowser__Smeli:SMc02569 3 LKARVIPCLDVKDGRVVKGVNFVDLIDAGDPVEAARAYDAAGADELCFLDITASSDNRETIFDVVARTAEQCFMP 77 778************************************************************************ PP TIGR00735 77 ltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaen.eeakyevtikgGr 150 ltvgGG+++++d++kll aGadkvsintaavk+pe+++e+ad+fG q+ivvaidak++ + e+ +e+ ++gGr lcl|FitnessBrowser__Smeli:SMc02569 78 LTVGGGVRQVADIRKLLLAGADKVSINTAAVKNPEFVAEAADKFGDQCIVVAIDAKKVSAQgEADRWEIFTHGGR 152 *******************************************************98765516689********* PP TIGR00735 151 estdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflkgkada 225 + t++d++e+a++v +lGaGeilltsmd+dGtksGyd++l++++++av+ PviasgG+G+ +h+ e++ +g+a a lcl|FitnessBrowser__Smeli:SMc02569 153 QPTGIDAIEFARKVVDLGAGEILLTSMDRDGTKSGYDISLTRAIADAVRAPVIASGGVGTLDHMVEGIRDGHATA 227 *************************************************************************** PP TIGR00735 226 aLaasvfhkreltieevkeylaergvkvr 254 +Laas+fh++ ++i+e k+++a++g+ +r lcl|FitnessBrowser__Smeli:SMc02569 228 VLAASIFHFGTYSIGEAKRHMAKHGIAMR 256 **************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (258 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: 8.60 // [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