Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate N515DRAFT_2934 N515DRAFT_2934 glutamine amidotransferase
Query= CharProtDB::CH_024511 (196 letters) >FitnessBrowser__Dyella79:N515DRAFT_2934 Length = 196 Score = 177 bits (450), Expect = 8e-50 Identities = 91/197 (46%), Positives = 129/197 (65%), Gaps = 2/197 (1%) Query: 1 MNVVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVRER 60 M VV++D G N+ SV+ A+ R G + ++ D + + AD++ LPGVG A M ++RE Sbjct: 1 MAVVLVDAGGTNIGSVRYALQRLGVDAALTSDANAIRQADRVILPGVGAAGPGMARLREL 60 Query: 61 ELFDLIKACTQPVLGICLGMQLLGRRSEESNGVDLLGIIDEDVPKMTDF-GLPLPHMGWN 119 L +LI++ TQPVLG+CLGMQLL RSEE + L +I + + GL +PHMGWN Sbjct: 61 GLVELIRSLTQPVLGVCLGMQLLFERSEEG-ATECLAVIPGAASRFAEAPGLRVPHMGWN 119 Query: 120 RVYPQAGNRLFQGIEDGAYFYFVHSYAMPVNPWTIAQCNYGEPFTAAVQKDNFYGVQFHP 179 R+ + + L G+ A+ YFVHSYA+P N T+A ++G F+A V + NF+G+QFHP Sbjct: 120 RLRVERAHPLVAGLGTDAWAYFVHSYAVPANDSTLATADFGGAFSAVVARGNFHGMQFHP 179 Query: 180 ERSGAAGAKLLKNFLEM 196 ERS GA+LLKNFLE+ Sbjct: 180 ERSAGVGARLLKNFLEL 196 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: 129 Number of extensions: 7 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: 196 Length of database: 196 Length adjustment: 20 Effective length of query: 176 Effective length of database: 176 Effective search space: 30976 Effective search space used: 30976 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 N515DRAFT_2934 N515DRAFT_2934 (glutamine amidotransferase)
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.6816.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-68 217.0 0.0 1.2e-68 216.8 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_2934 N515DRAFT_2934 glutamine amidotr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_2934 N515DRAFT_2934 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 216.8 0.0 1.2e-68 1.2e-68 1 197 [. 3 195 .. 3 196 .] 0.97 Alignments for each domain: == domain 1 score: 216.8 bits; conditional E-value: 1.2e-68 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaek 66 +v++d+g N+ sv+ al+r+g+ + +++d++++++ad+++lPGVGa+ +m++lrel+ l+e lcl|FitnessBrowser__Dyella79:N515DRAFT_2934 3 VVLVDAGGTNIGSVRYALQRLGVDAALTSDANAIRQADRVILPGVGAAGPGMARLRELG---LVEL 65 799*******************************************************9...4477 PP TIGR01855 67 vvkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek..kvPhiGWnevevvkesell 130 +++ ++pvlg+ClGmQllfe+seEg ++++l++i+g+ +++ ++ +vPh+GWn++ v ++++l+ lcl|FitnessBrowser__Dyella79:N515DRAFT_2934 66 IRSLTQPVLGVCLGMQLLFERSEEG-ATECLAVIPGAASRFAEAPglRVPHMGWNRLRVERAHPLV 130 8999********************6.68**************99899******************* PP TIGR01855 131 kgleeearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfl 196 +gl ++a +YfvHsYav+ ++ +la+ad+g f a+v+++n+ g+QFHPE+S+ +G++llknfl lcl|FitnessBrowser__Dyella79:N515DRAFT_2934 131 AGLGTDAWAYFVHSYAVPAND--STLATADFGGAFSAVVARGNFHGMQFHPERSAGVGARLLKNFL 194 ******************997..8*****************************************9 PP TIGR01855 197 e 197 e lcl|FitnessBrowser__Dyella79:N515DRAFT_2934 195 E 195 8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (196 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 4.99 // [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