Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_066326071.1 BLR17_RS13990 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q9X0C6 (253 letters) >NCBI__GCF_900100165.1:WP_066326071.1 Length = 251 Score = 295 bits (755), Expect = 6e-85 Identities = 149/251 (59%), Positives = 192/251 (76%), Gaps = 1/251 (0%) Query: 1 MLAKRIIACLDVKDGRVVKGTNFENLRDSGDPVELGKFYSEIGIDELVFLDITASVEKRK 60 ML KRII CLD+K+GR VKG NF +LRD+GDPVEL K YS+ G DELVFLDI+A+ E+R+ Sbjct: 1 MLTKRIIPCLDIKNGRTVKGVNFVDLRDAGDPVELAKIYSDEGADELVFLDISATEERRR 60 Query: 61 TMLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVSINTAAVENPSLITQIAQTF 120 T+++LV KVA I+IPFTVGGGI E L+ GADKVSIN++AV+NP LI +AQ F Sbjct: 61 TLVDLVRKVASTINIPFTVGGGISAVEDVEVLLQNGADKVSINSSAVKNPQLINDLAQKF 120 Query: 121 GSQAVVVAIDAKRVDGEFMVFTYSGKKNTGILLRDWVVEVEKRGAGEILLTSIDRDGTKS 180 GSQ VVVAIDAK++DG+++V GK T I L DW EVE+RGAGEIL TS+D DGTK+ Sbjct: 121 GSQCVVVAIDAKQIDGQWIVHLVGGKVPTEIRLFDWAQEVERRGAGEILFTSMDNDGTKN 180 Query: 181 GYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLAG-ADAALAASVFHFREIDVRELKE 239 G+ E + + L +PIIASGGAG ++HF+++F G ADAALAASVFHF+EI+++ LK Sbjct: 181 GFANEALAKLSNLVNIPIIASGGAGTIQHFVDSFTKGKADAALAASVFHFKEIEIKTLKN 240 Query: 240 YLKKHGVNVRL 250 L+ + + VR+ Sbjct: 241 ELRNNNIEVRI 251 Lambda K H 0.320 0.138 0.384 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: 216 Number of extensions: 3 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: 253 Length of database: 251 Length adjustment: 24 Effective length of query: 229 Effective length of database: 227 Effective search space: 51983 Effective search space used: 51983 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: 46 (22.3 bits)
Align candidate WP_066326071.1 BLR17_RS13990 (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.3554379.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-110 354.5 0.9 1.5e-110 354.4 0.9 1.0 1 NCBI__GCF_900100165.1:WP_066326071.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066326071.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 354.4 0.9 1.5e-110 1.5e-110 1 254 [] 1 250 [. 1 250 [. 0.99 Alignments for each domain: == domain 1 score: 354.4 bits; conditional E-value: 1.5e-110 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekv 73 ml+kriipCLd+k+gr vkGv+f +lrdaGdpvelak y++eGadelvfldi+a++e+r+t++++v++va ++ NCBI__GCF_900100165.1:WP_066326071.1 1 MLTKRIIPCLDIKNGRTVKGVNFVDLRDAGDPVELAKIYSDEGADELVFLDISATEERRRTLVDLVRKVASTI 73 8************************************************************************ PP TIGR00735 74 fiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeakyevti 146 iP+tvgGGi+ +edv+ ll+ Gadkvsin++avk+p+li++la++fGsq++vvaidak+ +++ v+ NCBI__GCF_900100165.1:WP_066326071.1 74 NIPFTVGGGISAVEDVEVLLQNGADKVSINSSAVKNPQLINDLAQKFGSQCVVVAIDAKQID----GQWIVHL 142 **********************************************************9765....68***** PP TIGR00735 147 kgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeafl 219 gG+ t++ +++wa+eve++GaGeil+tsmd+dGtk+G+ e l k+++ v+iP+iasgGaG+ +h+ ++f+ NCBI__GCF_900100165.1:WP_066326071.1 143 VGGKVPTEIRLFDWAQEVERRGAGEILFTSMDNDGTKNGFANEALAKLSNLVNIPIIASGGAGTIQHFVDSFT 215 ************************************************************************* PP TIGR00735 220 kgkadaaLaasvfhkreltieevkeylaergvkvr 254 kgkadaaLaasvfh++e++i+ +k+ l++++++vr NCBI__GCF_900100165.1:WP_066326071.1 216 KGKADAALAASVFHFKEIEIKTLKNELRNNNIEVR 250 **********************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (251 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: 21.30 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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