Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate Ac3H11_4731 Imidazole glycerol phosphate synthase amidotransferase subunit (EC 2.4.2.-)
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4731 Length = 220 Score = 288 bits (737), Expect = 5e-83 Identities = 141/215 (65%), Positives = 163/215 (75%), Gaps = 6/215 (2%) Query: 4 IVVVDYGMGNLRSVAQALRHVAPEAD--VRISGEVADIRAADRVVLPGQGAMPDCMRSLR 61 +VVVDYGMGNLRSV+QA++ A V ++ D+RAA RVVLPGQGAMPDCMR LR Sbjct: 6 VVVVDYGMGNLRSVSQAVQAAAQGTGWTVVVTQRPEDVRAAARVVLPGQGAMPDCMRELR 65 Query: 62 ESGVQDAVIEASRTKPLFGVCVGEQMLFDWSEEGDTPGLGLLPGKVVRFDLEGMRQDDGS 121 ESG+Q++V+EA+ TKPLFGVCVG QML D S EGDTPGL L+PG+V +FDL G Q DGS Sbjct: 66 ESGLQESVLEAAATKPLFGVCVGMQMLLDHSAEGDTPGLSLIPGEVRKFDLAGRTQPDGS 125 Query: 122 LFKVPQMGWNHVHQTSR----HPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDF 177 FKVPQMGWN V Q HP+W G+ DN++FYFVHS+YAVP AH GQ YG F Sbjct: 126 RFKVPQMGWNQVRQMEHAGAVHPVWAGVPDNSYFYFVHSFYAVPQNPAHCAGQADYGGVF 185 Query: 178 ACAVARDNIFATQFHPEKSASAGLQLYRNFVHWKP 212 A A+ARDNIFATQFHPEKSA GL LYRNF+HW P Sbjct: 186 AAAIARDNIFATQFHPEKSAEHGLALYRNFLHWNP 220 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: 220 Number of extensions: 7 Number of successful extensions: 3 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: 220 Length adjustment: 22 Effective length of query: 190 Effective length of database: 198 Effective search space: 37620 Effective search space used: 37620 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 Ac3H11_4731 (Imidazole glycerol phosphate synthase amidotransferase subunit (EC 2.4.2.-))
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.16446.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-63 197.7 0.0 1e-62 197.5 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4731 Imidazole glycerol phosphate syn Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4731 Imidazole glycerol phosphate synthase amidotransferase subunit (EC 2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 197.5 0.0 1e-62 1e-62 1 197 [. 6 217 .. 6 218 .. 0.89 Alignments for each domain: == domain 1 score: 197.5 bits; conditional E-value: 1e-62 TIGR01855 1 ivvidygvgNlksvkkaler....vgaesevvkdskelekadklvlPGVGafkeamkklrel 58 +vv+dyg+gNl+sv++a+++ +g +++v++ ++++ a ++vlPG Ga+ ++m++lre+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4731 6 VVVVDYGMGNLRSVSQAVQAaaqgTGWTVVVTQRPEDVRAAARVVLPGQGAMPDCMRELRES 67 79***********8777665221168899999999*************************** PP TIGR01855 59 elellaekvvkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek......... 111 +l+ +++++kp+ g+C+GmQ+l+++s Eg +++gl+li+g+v+k++ + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4731 68 GLQES-VLEAAATKPLFGVCVGMQMLLDHSAEG-DTPGLSLIPGEVRKFDLAGrtqpdgsrf 127 *6555.46788889******************7.68*************8665566788999 PP TIGR01855 112 kvPhiGWnevevvke....sellkgleeearvYfvHsYaveleeeeavlakadygekfvaav 169 kvP++GWn+v +++ +++ +g+ +++++YfvHs+++++++ ++ +adyg f aa+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4731 128 KVPQMGWNQVRQMEHagavHPVWAGVPDNSYFYFVHSFYAVPQNPAHCAGQADYGGVFAAAI 189 **********9887622335899*************************************** PP TIGR01855 170 ekdnivgvQFHPEkSgktGlkllknfle 197 ++dni+++QFHPEkS++ Gl+l +nfl+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4731 190 ARDNIFATQFHPEKSAEHGLALYRNFLH 217 **************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (220 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: 8.42 // [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