Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate CA265_RS19265 CA265_RS19265 imidazole glycerol phosphate synthase subunit HisH
Query= BRENDA::Q5NMD4 (213 letters) >FitnessBrowser__Pedo557:CA265_RS19265 Length = 207 Score = 146 bits (368), Expect = 3e-40 Identities = 92/201 (45%), Positives = 118/201 (58%), Gaps = 17/201 (8%) Query: 17 GNLRSVANALLASGLARENLVVTANPDEVLQADRVVLPGVGAFASCMQALKAIPDMVPAL 76 GN +SV N + G +++ +P+++LQA +V+LPGVG+F M+ L V AL Sbjct: 14 GNTKSVVNMINRLG---GEVIIANSPEDLLQAKKVILPGVGSFDVGMKELNE-HGWVEAL 69 Query: 77 EKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPL--RPNDPSCKVPHMGW 134 LEK P LGIC+GMQ D+ EE GV GLGWI GK+ +P +P KVPHMGW Sbjct: 70 NIVALEKKIPVLGICLGMQFFFDESEE-GVLPGLGWIPGKLIKFVSQPENP-IKVPHMGW 127 Query: 135 NQI------GLTTDSHPLLRAGEAYFLHSYAFVPEDESTLLATTEHGGLVTAAVGRDNIM 188 N I GL LR YF+HSY V ED + ++AT HG VTA+V +DNI Sbjct: 128 NAIKVYKSNGLFPIQDEELRY---YFVHSYHAVCEDANHVVATAYHGSDVTASVQKDNIY 184 Query: 189 GVQFHPEKSQSYGLEFLSRFL 209 G QFHPEKS +G+E L FL Sbjct: 185 GFQFHPEKSHRFGMELLKNFL 205 Lambda K H 0.318 0.136 0.409 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: 155 Number of extensions: 10 Number of successful extensions: 5 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: 213 Length of database: 207 Length adjustment: 21 Effective length of query: 192 Effective length of database: 186 Effective search space: 35712 Effective search space used: 35712 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 45 (21.9 bits)
Align candidate CA265_RS19265 CA265_RS19265 (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.19956.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-68 215.7 0.0 3.2e-68 215.5 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS19265 CA265_RS19265 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS19265 CA265_RS19265 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 215.5 0.0 3.2e-68 3.2e-68 5 197 .. 10 206 .. 6 207 .] 0.96 Alignments for each domain: == domain 1 score: 215.5 bits; conditional E-value: 3.2e-68 TIGR01855 5 dygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrele.lellaekvvkkk 71 + +gN ksv ++++r+g e+ ++++ ++l +a+k++lPGVG+f+ +mk+l+e++ +e+l+ + +kk lcl|FitnessBrowser__Pedo557:CA265_RS19265 10 NLSLGNTKSVVNMINRLGGEVIIANSPEDLLQAKKVILPGVGSFDVGMKELNEHGwVEALNIVALEKK 77 6789********************************************************9******* PP TIGR01855 72 kpvlgiClGmQllfekseEgkevkglglikgkvkkleaek....kvPhiGWnevevvkesellkglee 135 pvlgiClGmQ++f++seEg +glg+i+gk k+ ++ kvPh+GWn ++v k++ l+ +e lcl|FitnessBrowser__Pedo557:CA265_RS19265 78 IPVLGICLGMQFFFDESEEG-VLPGLGWIPGKLIKFVSQPenpiKVPHMGWNAIKVYKSNGLFPIQDE 144 *******************7.68*************98877899********************8899 PP TIGR01855 136 earvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 e r+YfvHsY++++e+ ++v+a+a +g++ +a+v+kdni+g+QFHPEkS+++G++llknfl+ lcl|FitnessBrowser__Pedo557:CA265_RS19265 145 ELRYYFVHSYHAVCEDANHVVATAYHGSDVTASVQKDNIYGFQFHPEKSHRFGMELLKNFLS 206 99**********************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (207 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 6.97 // [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