Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate Dsui_1416 Dsui_1416 imidazole glycerol phosphate synthase, glutamine amidotransferase subunit
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >FitnessBrowser__PS:Dsui_1416 Length = 212 Score = 257 bits (656), Expect = 1e-73 Identities = 125/212 (58%), Positives = 147/212 (69%) Query: 1 MNKIVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSL 60 M KI V+DYGMGNLRSV QAL HVA +V ++ + A + AA+RVV PGQGAMPDCM L Sbjct: 1 MGKIAVIDYGMGNLRSVWQALEHVAEGREVVVTADPAVVAAAERVVFPGQGAMPDCMAEL 60 Query: 61 RESGVQDAVIEASRTKPLFGVCVGEQMLFDWSEEGDTPGLGLLPGKVVRFDLEGMRQDDG 120 G++ AV++A++ KP G+C+G QMLF+ SEEGD PGLG+ G+V RF + M DG Sbjct: 61 DARGLRPAVLQAAKDKPFLGICIGLQMLFEHSEEGDVPGLGVFAGQVRRFPADKMVAADG 120 Query: 121 SLFKVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDFACA 180 S KVP MGWN V T H LWEGI D A FYFVHSYY P + A V G YG F CA Sbjct: 121 SRLKVPHMGWNQVRHTRPHALWEGIEDGARFYFVHSYYVTPEDPAVVAGTADYGIPFTCA 180 Query: 181 VARDNIFATQFHPEKSASAGLQLYRNFVHWKP 212 VARDNIFA Q HPEKSA GL L RNF+ W+P Sbjct: 181 VARDNIFAIQSHPEKSARDGLALLRNFIRWQP 212 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: 189 Number of extensions: 5 Number of successful extensions: 1 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: 212 Length adjustment: 21 Effective length of query: 191 Effective length of database: 191 Effective search space: 36481 Effective search space used: 36481 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 Dsui_1416 Dsui_1416 (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.9181.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 1.3e-68 216.8 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_1416 Dsui_1416 imidazole glycerol pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_1416 Dsui_1416 imidazole glycerol phosphate synthase, glutamine amidotransferase subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 216.8 0.0 1.3e-68 1.3e-68 1 198 [] 4 210 .. 4 210 .. 0.94 Alignments for each domain: == domain 1 score: 216.8 bits; conditional E-value: 1.3e-68 TIGR01855 1 ivvidygvgNlksvkkalerv..gaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkpvl 75 i+vidyg+gNl+sv +ale+v g e++v++d + a+++v+PG Ga+ ++m++l ++l+ +++k+kp+l lcl|FitnessBrowser__PS:Dsui_1416 4 IAVIDYGMGNLRSVWQALEHVaeGREVVVTADPAVVAAAERVVFPGQGAMPDCMAELDARGLRPA-VLQAAKDKPFL 79 79*****************9944567888889999**************************7666.56778889*** PP TIGR01855 76 giClGmQllfekseEgkevkglglikgkvkkleaek.........kvPhiGWnevevvkesellkgleeearvYfvH 143 giC+G+Q+lfe+seEg +v+glg++ g+v+++ a+k kvPh+GWn+v ++ ++l +g+e++ar+YfvH lcl|FitnessBrowser__PS:Dsui_1416 80 GICIGLQMLFEHSEEG-DVPGLGVFAGQVRRFPADKmvaadgsrlKVPHMGWNQVRHTRPHALWEGIEDGARFYFVH 155 ***************6.69**************998899999*9********************************* PP TIGR01855 144 sYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknflel 198 sY+v++e+ v +adyg f++av++dni+++Q HPEkS++ Gl+ll+nf+++ lcl|FitnessBrowser__PS:Dsui_1416 156 SYYVTPEDPAVVAGTADYGIPFTCAVARDNIFAIQSHPEKSARDGLALLRNFIRW 210 ****************************************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (212 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: 00:00:00.00 # Mc/sec: 5.55 // [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