Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate HSERO_RS21015 HSERO_RS21015 imidazole glycerol phosphate synthase
Query= CharProtDB::CH_024511 (196 letters) >FitnessBrowser__HerbieS:HSERO_RS21015 Length = 202 Score = 135 bits (339), Expect = 6e-37 Identities = 84/203 (41%), Positives = 117/203 (57%), Gaps = 11/203 (5%) Query: 3 VVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVRE--- 59 + I++ G NL S+ + R G + ++ DP+ V A+KL LPGVG AAM ++ E Sbjct: 2 ITIVNYGMGNLGSLLNMFKRIGVKARIESDPEAVRDAEKLVLPGVGAFDAAMHRINETPG 61 Query: 60 -RELFDLIKACTQ--PVLGICLGMQLLGRRSEESNGVDLLGIIDEDVPKMTDF-GLPLPH 115 R D KA + PV+G+CLGMQLL R SEE + LG ID + + GL +PH Sbjct: 62 LRAALDH-KALIERVPVIGVCLGMQLLTRSSEEGK-LPGLGWIDGEAIRFPRIDGLKVPH 119 Query: 116 MGWNRVYPQAGNRLFQGIEDGAYFYFVHSYAMPV-NP-WTIAQCNYGEPFTAAVQKDNFY 173 MGWN +P + L I +YFVHSY + V NP ++ + YG F +A+ +DN Y Sbjct: 120 MGWNVAHPATPSALTNDIGIEPRYYFVHSYFVKVDNPVHSLMRTQYGVEFDSAIGRDNIY 179 Query: 174 GVQFHPERSGAAGAKLLKNFLEM 196 G QFHPE+S G K+L+NF E+ Sbjct: 180 GAQFHPEKSHRFGMKILQNFAEL 202 Lambda K H 0.322 0.140 0.432 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: 131 Number of extensions: 6 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: 196 Length of database: 202 Length adjustment: 21 Effective length of query: 175 Effective length of database: 181 Effective search space: 31675 Effective search space used: 31675 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 HSERO_RS21015 HSERO_RS21015 (imidazole glycerol phosphate synthase)
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.24838.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-70 221.5 0.0 5.1e-70 221.4 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS21015 HSERO_RS21015 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS21015 HSERO_RS21015 imidazole glycerol phosphate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 221.4 0.0 5.1e-70 5.1e-70 1 197 [. 2 201 .. 2 202 .] 0.96 Alignments for each domain: == domain 1 score: 221.4 bits; conditional E-value: 5.1e-70 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrele..lellaek 66 i++++yg+gNl s+ ++++r+g+++++ +d +++++a+klvlPGVGaf++am++++e+ + +l +k lcl|FitnessBrowser__HerbieS:HSERO_RS21015 2 ITIVNYGMGNLGSLLNMFKRIGVKARIESDPEAVRDAEKLVLPGVGAFDAAMHRINETPglRAALDHK 69 78*******************************************************98866677888 PP TIGR01855 67 vvkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek..kvPhiGWnevevvkesellkg 132 + ++ pv+g+ClGmQll ++seEg + +glg+i+g+ ++ + kvPh+GWn ++++ s+l+++ lcl|FitnessBrowser__HerbieS:HSERO_RS21015 70 ALIERVPVIGVCLGMQLLTRSSEEG-KLPGLGWIDGEAIRFPRIDglKVPHMGWNVAHPATPSALTND 136 9999********************6.69*************998889********************* PP TIGR01855 133 leeearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 + e r+YfvHsY v++ + + l+ ++yg +f +a+ +dni+g+QFHPEkS+++G+k+l+nf+e lcl|FitnessBrowser__HerbieS:HSERO_RS21015 137 IGIEPRYYFVHSYFVKVDNPVHSLMRTQYGVEFDSAIGRDNIYGAQFHPEKSHRFGMKILQNFAE 201 ***************************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (202 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: 5.78 // [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