Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate WP_041376498.1 PNAP_RS03460 imidazole glycerol phosphate synthase subunit HisH
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >NCBI__GCF_000015505.1:WP_041376498.1 Length = 226 Score = 263 bits (671), Expect = 2e-75 Identities = 129/223 (57%), Positives = 159/223 (71%), Gaps = 11/223 (4%) Query: 1 MNKIVVVDYGMGNLRSVAQALRHVAPEA--DVRISGEVADIRAADRVVLPGQGAMPDCMR 58 + + VVDYG GNLRSV+QA+RHV +V ++ D+ A+RVVLPGQGAM DCM Sbjct: 4 LKTVAVVDYGSGNLRSVSQAVRHVVQGTGYEVLVTSNPQDVLNAERVVLPGQGAMHDCML 63 Query: 59 SLRESGVQDAVIEASRTKPLFGVCVGEQMLFDWSEEG----DTPGLGLLPGKVVRFDLEG 114 +L SG+ AV+ A+ KPLFGVCVG QML D S EG TPGLGL+ G+VV+FDL G Sbjct: 64 ALEHSGMLGAVLHAASHKPLFGVCVGMQMLLDNSHEGLDGAPTPGLGLIHGEVVKFDLAG 123 Query: 115 MRQDDGSLFKVPQMGWNHVHQT-----SRHPLWEGIADNAFFYFVHSYYAVPAESAHVVG 169 Q DGS FKVPQMGWN V+Q+ HP+W G+ D ++FYFVHS+YA P+++ H+ G Sbjct: 124 QLQPDGSRFKVPQMGWNQVYQSRPDGVQAHPVWAGVPDGSYFYFVHSFYACPSDARHIAG 183 Query: 170 QTPYGRDFACAVARDNIFATQFHPEKSASAGLQLYRNFVHWKP 212 + YG FA A+ARDNIFATQFHPEKSA GL LYRNF+HW P Sbjct: 184 EADYGGRFAAAIARDNIFATQFHPEKSADQGLALYRNFLHWNP 226 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: 212 Number of extensions: 8 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: 212 Length of database: 226 Length adjustment: 22 Effective length of query: 190 Effective length of database: 204 Effective search space: 38760 Effective search space used: 38760 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 WP_041376498.1 PNAP_RS03460 (imidazole glycerol phosphate synthase subunit HisH)
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.425.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-59 187.6 0.0 1.3e-59 187.4 0.0 1.0 1 lcl|NCBI__GCF_000015505.1:WP_041376498.1 PNAP_RS03460 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015505.1:WP_041376498.1 PNAP_RS03460 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 187.4 0.0 1.3e-59 1.3e-59 1 197 [. 7 223 .. 7 224 .. 0.89 Alignments for each domain: == domain 1 score: 187.4 bits; conditional E-value: 1.3e-59 TIGR01855 1 ivvidygvgNlksvkkalerv....gaesevvkdskelekadklvlPGVGafkeamkklrelelellae 65 ++v+dyg+gNl+sv++a+++v g+e+ v+++ +++ +a+++vlPG Ga++++m l++++ l a lcl|NCBI__GCF_000015505.1:WP_041376498.1 7 VAVVDYGSGNLRSVSQAVRHVvqgtGYEVLVTSNPQDVLNAERVVLPGQGAMHDCMLALEHSG-MLGAV 74 79***********77776553333399************************************.44446 PP TIGR01855 66 kvvkkkkpvlgiClGmQllfekseE...gkevkglglikgkvkkleaek.........kvPhiGWneve 122 +++++kp+ g+C+GmQ+l+++s+E g ++glgli+g+v+k++ + kvP++GWn+v lcl|NCBI__GCF_000015505.1:WP_041376498.1 75 LHAASHKPLFGVCVGMQMLLDNSHEgldGAPTPGLGLIHGEVVKFDLAGqlqpdgsrfKVPQMGWNQVY 143 899999*******************55556799***********98765667888999**********8 PP TIGR01855 123 v.....vkesellkgleeearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgk 186 v+++++ +g+ +++++YfvHs+++ +++ ++ adyg +f aa+++dni+++QFHPEkS++ lcl|NCBI__GCF_000015505.1:WP_041376498.1 144 QsrpdgVQAHPVWAGVPDGSYFYFVHSFYACPSDARHIAGEADYGGRFAAAIARDNIFATQFHPEKSAD 212 722233567899********************************************************* PP TIGR01855 187 tGlkllknfle 197 +Gl+l +nfl+ lcl|NCBI__GCF_000015505.1:WP_041376498.1 213 QGLALYRNFLH 223 *********86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (226 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: 5.16 // [ok]
This GapMind analysis is from Apr 10 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