Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate AO356_03385 AO356_03385 imidazole glycerol phosphate synthase subunit HisH
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_03385 Length = 202 Score = 166 bits (420), Expect = 3e-46 Identities = 93/207 (44%), Positives = 123/207 (59%), Gaps = 11/207 (5%) Query: 4 IVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSLRES 63 IVVVDYG+GN+ SV L+ V +A + S V DI A++++LPG GA M++LRES Sbjct: 2 IVVVDYGVGNIASVLNMLKRVGAKA--KSSNLVDDIVNAEKLILPGVGAFDAGMKTLRES 59 Query: 64 GVQDAVIEASRT--KPLFGVCVGEQMLFDWSEEGDTPGLGLLPGKVVRFDLEGMRQDDGS 121 G+ D + + KP+ GVC+G QML SEEG PGLG + + RF+ R Sbjct: 60 GLIDVLNQQVLVARKPVMGVCLGSQMLGRRSEEGVEPGLGWIDMDIKRFEKRPER----- 114 Query: 122 LFKVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDFACAV 181 KVP MGW+HV HPL G+ + + +YFVH YY P + YG+ F AV Sbjct: 115 --KVPHMGWSHVSCNYEHPLVRGLTEESRYYFVHGYYMCPDNERDTLLTADYGQKFTAAV 172 Query: 182 ARDNIFATQFHPEKSASAGLQLYRNFV 208 A+DNIF QFHPEKS G+QL++NFV Sbjct: 173 AKDNIFGFQFHPEKSHRFGMQLFKNFV 199 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: 144 Number of extensions: 5 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: 202 Length adjustment: 21 Effective length of query: 191 Effective length of database: 181 Effective search space: 34571 Effective search space used: 34571 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 AO356_03385 AO356_03385 (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.9658.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-78 248.5 0.0 2.8e-78 248.3 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03385 AO356_03385 imidazole glycerol p Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03385 AO356_03385 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 248.3 0.0 2.8e-78 2.8e-78 1 197 [. 2 200 .. 2 201 .. 0.98 Alignments for each domain: == domain 1 score: 248.3 bits; conditional E-value: 2.8e-78 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrele.lel 62 ivv+dygvgN++sv ++l+rvga+++ ++ +++ +a+kl+lPGVGaf+++mk+lre++ +++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03385 2 IVVVDYGVGNIASVLNMLKRVGAKAKSSNLVDDIVNAEKLILPGVGAFDAGMKTLRESGlIDV 64 89*********************************************************9*** PP TIGR01855 63 laekvvkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek..kvPhiGWnevev 123 l+++v ++kpv+g+ClG Q+l ++seEg ++glg+i++++k++e++ kvPh+GW +v+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03385 65 LNQQVLVARKPVMGVCLGSQMLGRRSEEGV-EPGLGWIDMDIKRFEKRPerKVPHMGWSHVSC 126 ****************************75.7**************99889************ PP TIGR01855 124 vkesellkgleeearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgk 186 e++l++gl+ee+r+YfvH Y++ + +e ++l +adyg+kf+aav+kdni+g+QFHPEkS++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03385 127 NYEHPLVRGLTEESRYYFVHGYYMCPDNERDTLLTADYGQKFTAAVAKDNIFGFQFHPEKSHR 189 *************************************************************** PP TIGR01855 187 tGlkllknfle 197 +G++l+knf+e lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03385 190 FGMQLFKNFVE 200 *********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (202 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: 6.46 // [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