Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_010527312.1 GQW_RS0107125 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q9X0C6 (253 letters) >NCBI__GCF_000220155.1:WP_010527312.1 Length = 251 Score = 262 bits (670), Expect = 4e-75 Identities = 138/251 (54%), Positives = 179/251 (71%), Gaps = 2/251 (0%) Query: 1 MLAKRIIACLDVKDGRVVKGTNFENLRDSGDPVELGKFYSEIGIDELVFLDITASVEKRK 60 ML+KRII CLD+++G+ VKG F ++++ GDPVELG Y+ G DELVFLDITAS EKRK Sbjct: 1 MLSKRIIPCLDIRNGKTVKGVKFLDIKEVGDPVELGALYARQGADELVFLDITASHEKRK 60 Query: 61 TMLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVSINTAAVENPSLITQIAQTF 120 T +LV ++A+ I+IPFTVGGGI + + A L+ GADK+SIN++AV NP LI+ +A+ F Sbjct: 61 TFADLVLRIAQHINIPFTVGGGISELKDAEILLNAGADKISINSSAVRNPQLISDMAKHF 120 Query: 121 GSQAVVVAIDAKRV-DGEFMVFTYSGKKNTGILLRDWVVEVEKRGAGEILLTSIDRDGTK 179 GSQ VVVAIDAK+V D +++V G+ T L W E E RGAGEIL TS+D DG K Sbjct: 121 GSQFVVVAIDAKQVEDDDWVVTVNGGRIPTEKRLFSWAREAEDRGAGEILFTSMDHDGVK 180 Query: 180 SGYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLAG-ADAALAASVFHFREIDVRELK 238 G+ E + + ++PIIASGGAG EHF + F G ADA LAAS+FHF EI + ELK Sbjct: 181 KGFANEALARLSEELSIPIIASGGAGAKEHFKDVFTIGKADAGLAASIFHFNEIPIPELK 240 Query: 239 EYLKKHGVNVR 249 +YL+ H + VR Sbjct: 241 DYLRSHNIPVR 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: 222 Number of extensions: 7 Number of successful extensions: 5 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_010527312.1 GQW_RS0107125 (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.3631640.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-107 343.8 0.0 2.9e-107 343.7 0.0 1.0 1 NCBI__GCF_000220155.1:WP_010527312.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000220155.1:WP_010527312.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 343.7 0.0 2.9e-107 2.9e-107 1 254 [] 1 251 [] 1 251 [] 0.99 Alignments for each domain: == domain 1 score: 343.7 bits; conditional E-value: 2.9e-107 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekv 73 ml+kriipCLd+++g+ vkGv+f +++++Gdpvel + y+++Gadelvflditas+ekr+t ++v r+a+++ NCBI__GCF_000220155.1:WP_010527312.1 1 MLSKRIIPCLDIRNGKTVKGVKFLDIKEVGDPVELGALYARQGADELVFLDITASHEKRKTFADLVLRIAQHI 73 89*********************************************************************** PP TIGR00735 74 fiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeakyevti 146 iP+tvgGGi++++d++ ll+aGadk+sin++av++p+li+++a++fGsq +vvaidak++++ + vt+ NCBI__GCF_000220155.1:WP_010527312.1 74 NIPFTVGGGISELKDAEILLNAGADKISINSSAVRNPQLISDMAKHFGSQFVVVAIDAKQVEDD---DWVVTV 143 ***********************************************************99876...6***** PP TIGR00735 147 kgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeafl 219 +gGr t+ +++wa+e+e++GaGeil+tsmd+dG+k+G+ e l +++e+++iP+iasgGaG++eh++++f+ NCBI__GCF_000220155.1:WP_010527312.1 144 NGGRIPTEKRLFSWAREAEDRGAGEILFTSMDHDGVKKGFANEALARLSEELSIPIIASGGAGAKEHFKDVFT 216 ************************************************************************* PP TIGR00735 220 kgkadaaLaasvfhkreltieevkeylaergvkvr 254 gkada Laas+fh++e+ i e+k+yl++++++vr NCBI__GCF_000220155.1:WP_010527312.1 217 IGKADAGLAASIFHFNEIPIPELKDYLRSHNIPVR 251 *********************************98 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: 16.95 // [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