Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate Echvi_2516 Echvi_2516 imidazoleglycerol phosphate synthase, cyclase subunit
Query= BRENDA::Q9X0C6 (253 letters) >FitnessBrowser__Cola:Echvi_2516 Length = 251 Score = 284 bits (726), Expect = 1e-81 Identities = 146/251 (58%), Positives = 183/251 (72%), Gaps = 1/251 (0%) Query: 1 MLAKRIIACLDVKDGRVVKGTNFENLRDSGDPVELGKFYSEIGIDELVFLDITASVEKRK 60 ML KRII CLD+K+GR VKG NF +LRD+GDPVEL K YS+ G DELVFLDITA+V+KRK Sbjct: 1 MLTKRIIPCLDIKEGRTVKGVNFVDLRDAGDPVELAKVYSDEGADELVFLDITATVDKRK 60 Query: 61 TMLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVSINTAAVENPSLITQIAQTF 120 T+ ELV +VA+ I+IPFTVGGGI E L+ GADK+SIN+AAV+ P +I ++A F Sbjct: 61 TLAELVTRVAKAINIPFTVGGGISTVEDVKVLLNAGADKISINSAAVKRPEVIDEMAAEF 120 Query: 121 GSQAVVVAIDAKRVDGEFMVFTYSGKKNTGILLRDWVVEVEKRGAGEILLTSIDRDGTKS 180 GSQ +VVAID + VDG +V T+ G+K T + + W EV RGAGEILLTS+D DGTK+ Sbjct: 121 GSQCIVVAIDTRNVDGVDLVHTHGGRKPTTLQTQAWAKEVADRGAGEILLTSMDHDGTKA 180 Query: 181 GYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLAG-ADAALAASVFHFREIDVRELKE 239 G+ + + T+P+IASGGAG M HF F AG ADAALAAS+FHF+EI + LK Sbjct: 181 GFADGLTSEISAALTIPVIASGGAGTMPHFKSVFTAGKADAALAASIFHFKEIGIPALKH 240 Query: 240 YLKKHGVNVRL 250 YL GV +R+ Sbjct: 241 YLAGEGVTMRI 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: 228 Number of extensions: 8 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: 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 Echvi_2516 Echvi_2516 (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.18228.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-112 358.3 2.2 1.1e-111 358.2 2.2 1.0 1 lcl|FitnessBrowser__Cola:Echvi_2516 Echvi_2516 imidazoleglycerol pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2516 Echvi_2516 imidazoleglycerol phosphate synthase, cyclase subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 358.2 2.2 1.1e-111 1.1e-111 1 254 [] 1 250 [. 1 250 [. 0.99 Alignments for each domain: == domain 1 score: 358.2 bits; conditional E-value: 1.1e-111 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvf 74 ml+kriipCLd+k+gr vkGv+f +lrdaGdpvelak+y++eGadelvfldita+ +kr+t+ e+v+rva+ + lcl|FitnessBrowser__Cola:Echvi_2516 1 MLTKRIIPCLDIKEGRTVKGVNFVDLRDAGDPVELAKVYSDEGADELVFLDITATVDKRKTLAELVTRVAKAIN 74 8************************************************************************* PP TIGR00735 75 iPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeakyevtikg 148 iP+tvgGGi+++edvk ll+aGadk+sin+aavk+pe+i e+a fGsq+ivvaid++++ + v+++g lcl|FitnessBrowser__Cola:Echvi_2516 75 IPFTVGGGISTVEDVKVLLNAGADKISINSAAVKRPEVIDEMAAEFGSQCIVVAIDTRNVDGVD----LVHTHG 144 *********************************************************9987654....89**** PP TIGR00735 149 GrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflkgk 222 Gr+ t l++ +wakev+++GaGeilltsmd+dGtk+G+ l+ +++ a++iPviasgGaG++ h++ +f++gk lcl|FitnessBrowser__Cola:Echvi_2516 145 GRKPTTLQTQAWAKEVADRGAGEILLTSMDHDGTKAGFADGLTSEISAALTIPVIASGGAGTMPHFKSVFTAGK 218 ************************************************************************** PP TIGR00735 223 adaaLaasvfhkreltieevkeylaergvkvr 254 adaaLaas+fh++e+ i +k+yla +gv++r lcl|FitnessBrowser__Cola:Echvi_2516 219 ADAALAASIFHFKEIGIPALKHYLAGEGVTMR 250 *****************************998 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.28 // [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