Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate GFF153 Psest_0153 imidazole glycerol phosphate synthase, glutamine amidotransferase subunit
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >FitnessBrowser__psRCH2:GFF153 Length = 212 Score = 196 bits (499), Expect = 2e-55 Identities = 105/211 (49%), Positives = 127/211 (60%), Gaps = 4/211 (1%) Query: 1 MNKIVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSL 60 M + V+DYGMGNL SVA+AL HV V I+ + IR ADRVV PG GA+ DCM + Sbjct: 1 MQTVAVIDYGMGNLHSVAKALEHVGA-GRVLITSDAQVIREADRVVFPGVGAIRDCMAEI 59 Query: 61 RESGVQDAVIEASRTKPLFGVCVGEQMLFDWSEEGD-TPGLGLLPGKVVRFDLEGMRQDD 119 R G + V E S+ +P G+CVG Q L + SEE + +GL PG+V F + +D Sbjct: 60 RRLGFDELVREVSQDRPFLGICVGMQALMERSEENEGVDCIGLFPGQVRFFGKD--LHED 117 Query: 120 GSLFKVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDFAC 179 G KVP MGWN V Q HPLW I DN FYFVHSYY VVG+ YG DFA Sbjct: 118 GEHLKVPHMGWNEVKQVVDHPLWHAIPDNGRFYFVHSYYIEAGNPRQVVGRGHYGNDFAA 177 Query: 180 AVARDNIFATQFHPEKSASAGLQLYRNFVHW 210 A+A + FA QFHPEKS + GLQL +NF W Sbjct: 178 ALADGSRFAVQFHPEKSHTHGLQLLQNFAAW 208 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: 172 Number of extensions: 6 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: 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 GFF153 Psest_0153 (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.7304.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-70 220.6 0.0 9.9e-70 220.4 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF153 Psest_0153 imidazole glycerol ph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF153 Psest_0153 imidazole glycerol phosphate synthase, glutamine amidotransferase subun # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 220.4 0.0 9.9e-70 9.9e-70 1 197 [. 4 207 .. 4 208 .. 0.95 Alignments for each domain: == domain 1 score: 220.4 bits; conditional E-value: 9.9e-70 TIGR01855 1 ivvidygvgNlksvkkalervgaes.evvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkpvl 75 ++vidyg+gNl+sv+kale+vga +++d++ +++ad++v+PGVGa +++m+++r+l+ + l ++v++++p+l lcl|FitnessBrowser__psRCH2:GFF153 4 VAVIDYGMGNLHSVAKALEHVGAGRvLITSDAQVIREADRVVFPGVGAIRDCMAEIRRLGFDEL-VREVSQDRPFL 78 79********************9651578899****************************8888.46677888*** PP TIGR01855 76 giClGmQllfekseEgkevkglglikgkvkkleaek.......kvPhiGWnevevvkesellkgleeearvYfvHs 144 giC+GmQ l+e+seE++ v+++gl++g+v+ + ++ kvPh+GWnev+ v +++l + + ++ r+YfvHs lcl|FitnessBrowser__psRCH2:GFF153 79 GICVGMQALMERSEENEGVDCIGLFPGQVRFFGKDLhedgehlKVPHMGWNEVKQVVDHPLWHAIPDNGRFYFVHS 154 *****************************99988777788999********************************* PP TIGR01855 145 YaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 Y++e + +v+ +yg++f aa++++ ++vQFHPEkS++ Gl+ll+nf++ lcl|FitnessBrowser__psRCH2:GFF153 155 YYIEAGNPRQVVGRGHYGNDFAAALADGSRFAVQFHPEKSHTHGLQLLQNFAA 207 ***************************************************86 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.95 // [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