Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate GFF3067 HP15_3011 imidazole glycerol phosphate synthase subunit HisH
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >FitnessBrowser__Marino:GFF3067 Length = 225 Score = 210 bits (534), Expect = 2e-59 Identities = 107/211 (50%), Positives = 131/211 (62%), Gaps = 3/211 (1%) Query: 1 MNKIVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSL 60 M + ++DYGMGNL S +A+ HVAP+ V ++ IR ADRV+LPG GA+ DCM + Sbjct: 13 MKTVAIIDYGMGNLHSAKKAVEHVAPDTTVLVTDNAEKIREADRVILPGVGAIRDCMAEM 72 Query: 61 RESGVQDAVIEASRTKPLFGVCVGEQMLFDWSEE-GDTPGLGLLPGKVVRFDLEGMRQDD 119 GV D V E S+ +P G+CVG Q L SEE G +GL P +V F ++ Sbjct: 73 HRLGVVDLVREVSQDRPFLGICVGMQALMSRSEENGGVDCIGLFPSQVRYFG--DHLTEN 130 Query: 120 GSLFKVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDFAC 179 G KVP MGWN V QT HPLW I + FYFVHS+YA +A + G+T YG D A Sbjct: 131 GERLKVPHMGWNQVQQTIDHPLWHNIPEGDRFYFVHSFYAEAEGNADMAGRTRYGVDLAA 190 Query: 180 AVARDNIFATQFHPEKSASAGLQLYRNFVHW 210 AVARDNIFA QFHPEKSA AGLQL NF +W Sbjct: 191 AVARDNIFAVQFHPEKSARAGLQLLENFTNW 221 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: 171 Number of extensions: 6 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: 212 Length of database: 225 Length adjustment: 22 Effective length of query: 190 Effective length of database: 203 Effective search space: 38570 Effective search space used: 38570 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 GFF3067 HP15_3011 (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.12272.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-68 216.1 0.0 2.5e-68 215.9 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF3067 HP15_3011 imidazole glycerol pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF3067 HP15_3011 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 215.9 0.0 2.5e-68 2.5e-68 1 197 [. 16 220 .. 16 221 .. 0.92 Alignments for each domain: == domain 1 score: 215.9 bits; conditional E-value: 2.5e-68 TIGR01855 1 ivvidygvgNlksvkkalervg..aesevvkdskelekadklvlPGVGafkeamkklrele.lellaekvvkkkk 72 +++idyg+gNl+s kka+e+v +++ v+++++++++ad+++lPGVGa +++m+++++l+ ++l+ ++v++++ lcl|FitnessBrowser__Marino:GFF3067 16 VAIIDYGMGNLHSAKKAVEHVApdTTVLVTDNAEKIREADRVILPGVGAIRDCMAEMHRLGvVDLV--REVSQDR 88 79******************97214555677789***************************55555..6788899 PP TIGR01855 73 pvlgiClGmQllfekseEgkevkglglikgkvkkleaek.......kvPhiGWnevevvkesellkgleeearvY 140 p+lgiC+GmQ l+++seE++ v+++gl++ +v+ + ++ kvPh+GWn+v+ + +++l +++ e++r+Y lcl|FitnessBrowser__Marino:GFF3067 89 PFLGICVGMQALMSRSEENGGVDCIGLFPSQVRYFGDHLtengerlKVPHMGWNQVQQTIDHPLWHNIPEGDRFY 163 ********************************98877666667899***************************** PP TIGR01855 141 fvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 fvHs+++e e + ++ + yg ++ aav++dni++vQFHPEkS+++Gl+ll+nf++ lcl|FitnessBrowser__Marino:GFF3067 164 FVHSFYAEAEGNADMAGRTRYGVDLAAAVARDNIFAVQFHPEKSARAGLQLLENFTN 220 *******************************************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (225 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: 9.50 // [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