Align Imidazole glycerol phosphate synthase subunit HisF; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF; EC 4.3.2.10 (characterized)
to candidate Synpcc7942_2087 Synpcc7942_2087 imidazole glycerol phosphate synthase subunit HisF
Query= SwissProt::Q7SIB9 (252 letters) >FitnessBrowser__SynE:Synpcc7942_2087 Length = 255 Score = 301 bits (771), Expect = 9e-87 Identities = 160/253 (63%), Positives = 194/253 (76%), Gaps = 5/253 (1%) Query: 3 LAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEERAI 62 LAKRI+PCLDV AGRVVKGVNFV+LRDAGDPVE A+AYD AGADELVFLDI+ATHEER I Sbjct: 2 LAKRILPCLDVKAGRVVKGVNFVDLRDAGDPVELAQAYDAAGADELVFLDIAATHEERQI 61 Query: 63 LLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADHFG 122 L+DVV R AE+VFIPLTVGGG+ LE R+LL +GADKVS+NSAAVR P+LIR +D FG Sbjct: 62 LVDVVYRTAEQVFIPLTVGGGINDLETIRQLLRAGADKVSINSAAVRDPDLIRRASDRFG 121 Query: 123 AQAVVLAIDARWRGDFP----EVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMDRDG 178 +Q +V+AIDAR R D +V+V GGR TG+ A+ WA GAGE+L+TSMD DG Sbjct: 122 SQCIVVAIDARRRTDPDNPGWDVYVRGGRENTGIDALTWAETVARNGAGELLVTSMDADG 181 Query: 179 TKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQAG-AEAALAASVFHFGEIPIPK 237 T+ GYDL LTR +A+ V +PVIASGGAG E EAF+ G AEAAL AS+ H+G++ I + Sbjct: 182 TQAGYDLELTRAIADRVEIPVIASGGAGTCEDIAEAFRTGHAEAALLASLLHYGQLTIAE 241 Query: 238 LKRYLAEKGVHVR 250 +K +L + R Sbjct: 242 IKDHLRSAQIPTR 254 Lambda K H 0.321 0.138 0.398 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: 237 Number of extensions: 15 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: 252 Length of database: 255 Length adjustment: 24 Effective length of query: 228 Effective length of database: 231 Effective search space: 52668 Effective search space used: 52668 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 (21.9 bits) S2: 47 (22.7 bits)
Align candidate Synpcc7942_2087 Synpcc7942_2087 (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.14800.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-120 386.3 0.2 3e-120 386.2 0.2 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_2087 Synpcc7942_2087 imidazole glycer Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_2087 Synpcc7942_2087 imidazole glycerol phosphate synthase subunit HisF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 386.2 0.2 3e-120 3e-120 1 254 [] 1 254 [. 1 254 [. 0.99 Alignments for each domain: == domain 1 score: 386.2 bits; conditional E-value: 3e-120 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 mlakri+pCLdvk+grvvkGv+f +lrdaGdpvela++yd+ Gadelvfldi+a++e+r+++++vv r+ lcl|FitnessBrowser__SynE:Synpcc7942_2087 1 MLAKRILPCLDVKAGRVVKGVNFVDLRDAGDPVELAQAYDAAGADELVFLDIAATHEERQILVDVVYRT 69 8******************************************************************** PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaene 138 ae+vfiPltvgGGi+++e +++llraGadkvsin+aav++p+li++++drfGsq+ivvaida+r+++ + lcl|FitnessBrowser__SynE:Synpcc7942_2087 70 AEQVFIPLTVGGGINDLETIRQLLRAGADKVSINSAAVRDPDLIRRASDRFGSQCIVVAIDARRRTDPD 138 ********************************************************************* PP TIGR00735 139 eakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgG 207 + ++v+++gGre+t++d+++wa+ v++ GaGe+l+tsmd+dGt++Gydlel+++++++v+iPviasgG lcl|FitnessBrowser__SynE:Synpcc7942_2087 139 NPGWDVYVRGGRENTGIDALTWAETVARNGAGELLVTSMDADGTQAGYDLELTRAIADRVEIPVIASGG 207 ********************************************************************* PP TIGR00735 208 aGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 aG++e ++eaf +g+a+aaL as++h+++lti e+k++l++ +++ r lcl|FitnessBrowser__SynE:Synpcc7942_2087 208 AGTCEDIAEAFRTGHAEAALLASLLHYGQLTIAEIKDHLRSAQIPTR 254 *****************************************999876 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.96 // [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