Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate Ga0059261_3124 Ga0059261_3124 imidazole glycerol phosphate synthase, glutamine amidotransferase subunit
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >FitnessBrowser__Korea:Ga0059261_3124 Length = 204 Score = 157 bits (396), Expect = 2e-43 Identities = 90/207 (43%), Positives = 122/207 (58%), Gaps = 10/207 (4%) Query: 4 IVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSLRES 63 I + DYG+GN+R+ + + DV ++ A++ A R++LPG GA M L S Sbjct: 2 ITIADYGLGNIRAFVNIYKKL--NIDVAVAQTAAELELASRIILPGVGAFDWAMARLNAS 59 Query: 64 GVQDAVIEA--SRTKPLFGVCVGEQMLFDWSEEGDTPGLGLLPGKVVRFDL-EGMRQDDG 120 G++D + E R P+FGVCVG QM+ S+EG+ PGLG L +VVRFD+ EG RQ Sbjct: 60 GLRDTLDELVLGRKLPVFGVCVGMQMMCKRSDEGELPGLGWLDAEVVRFDVGEGSRQG-- 117 Query: 121 SLFKVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDFACA 180 ++P MGWN V + L+EG+ D+ YF+HSYY P + A + QT YG F A Sbjct: 118 --LQLPHMGWNDVAPVATDSLFEGL-DDWRCYFLHSYYVRPIDPAITLAQTNYGGLFTSA 174 Query: 181 VARDNIFATQFHPEKSASAGLQLYRNF 207 V N+ ATQFHPEKS G+ L RNF Sbjct: 175 VRSGNVCATQFHPEKSHGWGVALLRNF 201 Lambda K H 0.322 0.137 0.431 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: 147 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: 212 Length of database: 204 Length adjustment: 21 Effective length of query: 191 Effective length of database: 183 Effective search space: 34953 Effective search space used: 34953 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: 45 (21.9 bits)
Align candidate Ga0059261_3124 Ga0059261_3124 (imidazole glycerol phosphate synthase, glutamine amidotransferase subunit)
to HMM TIGR01855 (hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (EC 2.4.2.-))
# 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/TIGR01855.hmm # target sequence database: /tmp/gapView.14822.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01855 [M=198] Accession: TIGR01855 Description: IMP_synth_hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-63 200.4 0.0 1.5e-63 200.3 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_3124 Ga0059261_3124 imidazole glycero Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_3124 Ga0059261_3124 imidazole glycerol phosphate synthase, glutamine amidotransf # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 200.3 0.0 1.5e-63 1.5e-63 1 196 [. 2 202 .. 2 204 .] 0.96 Alignments for each domain: == domain 1 score: 200.3 bits; conditional E-value: 1.5e-63 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrele.lellaekvv 68 i++ dyg+gN++++ ++ ++++ + v++++ ele a +++lPGVGaf+ am++l+ ++ +++l e v lcl|FitnessBrowser__Korea:Ga0059261_3124 2 ITIADYGLGNIRAFVNIYKKLNIDVAVAQTAAELELASRIILPGVGAFDWAMARLNASGlRDTLDELVL 70 6899*******************************************************8888888999 PP TIGR01855 69 kkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek......kvPhiGWnevevvkesellk 131 +k pv g+C+GmQ++ ++s+Eg e +glg+++ +v++++ + ++Ph+GWn v +v+ ++l++ lcl|FitnessBrowser__Korea:Ga0059261_3124 71 GRKLPVFGVCVGMQMMCKRSDEG-ELPGLGWLDAEVVRFDVGEgsrqglQLPHMGWNDVAPVATDSLFE 138 9999******************6.79*************9766677799******************** PP TIGR01855 132 gleeearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfl 196 gl++ Yf+HsY+v++ + +la+++yg f++av+++n++++QFHPEkS+ G++ll+nf+ lcl|FitnessBrowser__Korea:Ga0059261_3124 139 GLDDWR-CYFLHSYYVRPIDPAITLAQTNYGGLFTSAVRSGNVCATQFHPEKSHGWGVALLRNFA 202 **9765.********************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (204 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: 7.19 // [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