Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate BPHYT_RS17690 BPHYT_RS17690 imidazole glycerol phosphate synthase
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >FitnessBrowser__BFirm:BPHYT_RS17690 Length = 213 Score = 342 bits (878), Expect = 2e-99 Identities = 165/209 (78%), Positives = 175/209 (83%) Query: 4 IVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSLRES 63 I +VDYGMGNLRSVAQALR APEADV I + IRAADRVVLPGQGAMPDCMRSL ES Sbjct: 5 IAIVDYGMGNLRSVAQALRKAAPEADVAIVDQPEAIRAADRVVLPGQGAMPDCMRSLAES 64 Query: 64 GVQDAVIEASRTKPLFGVCVGEQMLFDWSEEGDTPGLGLLPGKVVRFDLEGMRQDDGSLF 123 G+QDAVIEASR+KPL GVCVGEQMLFDWS EG TPGLGLLPGKV+RFDLEG QDDGS F Sbjct: 65 GLQDAVIEASRSKPLMGVCVGEQMLFDWSAEGGTPGLGLLPGKVLRFDLEGQLQDDGSRF 124 Query: 124 KVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDFACAVAR 183 KVPQMGWN V Q HPLW+G+ADNAFFYFVHSYY VP AH G+T YG F AVAR Sbjct: 125 KVPQMGWNRVRQAQPHPLWDGVADNAFFYFVHSYYVVPDNVAHTSGETVYGVPFTSAVAR 184 Query: 184 DNIFATQFHPEKSASAGLQLYRNFVHWKP 212 DNIFATQFHPEKSA AGL++YRNFVHW P Sbjct: 185 DNIFATQFHPEKSAEAGLRVYRNFVHWNP 213 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: 241 Number of extensions: 3 Number of successful extensions: 1 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: 213 Length adjustment: 21 Effective length of query: 191 Effective length of database: 192 Effective search space: 36672 Effective search space used: 36672 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 BPHYT_RS17690 BPHYT_RS17690 (imidazole glycerol phosphate synthase)
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.19704.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-63 199.9 0.0 2.1e-63 199.7 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS17690 BPHYT_RS17690 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS17690 BPHYT_RS17690 imidazole glycerol phosphate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 199.7 0.0 2.1e-63 2.1e-63 1 197 [. 5 210 .. 5 211 .. 0.92 Alignments for each domain: == domain 1 score: 199.7 bits; conditional E-value: 2.1e-63 TIGR01855 1 ivvidygvgNlksvkkalerv..gaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvv 68 i+++dyg+gNl+sv++al+++ +a + +v++ ++++ ad++vlPG Ga+ ++m++l e++l+ + ++ lcl|FitnessBrowser__BFirm:BPHYT_RS17690 5 IAIVDYGMGNLRSVAQALRKAapEADVAIVDQPEAIRAADRVVLPGQGAMPDCMRSLAESGLQDAVIEA- 73 79****************998335667788999****************************77775554. PP TIGR01855 69 kkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek.........kvPhiGWnevevvkesel 129 +++kp++g+C+G Q+lf+ s Eg+ ++glgl++gkv +++ e kvP++GWn+v ++ ++l lcl|FitnessBrowser__BFirm:BPHYT_RS17690 74 SRSKPLMGVCVGEQMLFDWSAEGG-TPGLGLLPGKVLRFDLEGqlqddgsrfKVPQMGWNRVRQAQPHPL 142 5567******************75.7************98776677888999****************** PP TIGR01855 130 lkgleeearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 g+ ++a +YfvHsY+v++ + ++ + yg f++av++dni+++QFHPEkS+++Gl++ +nf++ lcl|FitnessBrowser__BFirm:BPHYT_RS17690 143 WDGVADNAFFYFVHSYYVVPDNVAHTSGETVYGVPFTSAVARDNIFATQFHPEKSAEAGLRVYRNFVH 210 ******************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (213 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: 6.28 // [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