Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate Echvi_2514 Echvi_2514 imidazole glycerol phosphate synthase, glutamine amidotransferase subunit
Query= CharProtDB::CH_024511 (196 letters) >FitnessBrowser__Cola:Echvi_2514 Length = 194 Score = 144 bits (363), Expect = 1e-39 Identities = 83/197 (42%), Positives = 116/197 (58%), Gaps = 4/197 (2%) Query: 1 MNVVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVRER 60 M+V I+ N+ SV A+ R G ++ D + + ADK+ PG G A +AM +RER Sbjct: 1 MDVAIIKYNSGNVLSVLYALERLGINANLTDDVEEIKKADKVIFPGQGEASSAMRYLRER 60 Query: 61 ELFDLIKACTQPVLGICLGMQLLGRRSEESNGVDLLGIIDEDVPKMTDFGLPLPHMGWNR 120 L LIK QP GICLG QLL SEE N + LG+ V K +PH+GWN Sbjct: 61 NLDQLIKDLKQPFFGICLGQQLLCEYSEE-NDTECLGVFPVKVRKFPPAD-KVPHVGWNS 118 Query: 121 VYPQAGNRLFQGIEDGAYFYFVHSYAMPVNP-WTIAQCNYGEPFTAAVQKDNFYGVQFHP 179 + G +L +GI Y Y+VHSY ++P +T+A+ +Y E F+A +QKDNFY +Q HP Sbjct: 119 LQETQG-QLLEGINTHDYVYYVHSYFAEIHPEFTVAKTHYIEDFSALLQKDNFYAMQAHP 177 Query: 180 ERSGAAGAKLLKNFLEM 196 E+S +G K+L NFL++ Sbjct: 178 EKSSHSGQKILTNFLKL 194 Lambda K H 0.322 0.140 0.432 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: 117 Number of extensions: 6 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: 196 Length of database: 194 Length adjustment: 20 Effective length of query: 176 Effective length of database: 174 Effective search space: 30624 Effective search space used: 30624 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: 44 (21.6 bits)
Align candidate Echvi_2514 Echvi_2514 (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.3404.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-64 201.8 0.0 5.5e-64 201.7 0.0 1.0 1 lcl|FitnessBrowser__Cola:Echvi_2514 Echvi_2514 imidazole glycerol ph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2514 Echvi_2514 imidazole glycerol phosphate synthase, glutamine amidotransferase sub # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 201.7 0.0 5.5e-64 5.5e-64 1 197 [. 3 193 .. 3 194 .] 0.96 Alignments for each domain: == domain 1 score: 201.7 bits; conditional E-value: 5.5e-64 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkpv 74 +++i y++gN+ sv aler+g ++++++d +e++kadk+++PG G++++am+ lre++l++l ++ k+p+ lcl|FitnessBrowser__Cola:Echvi_2514 3 VAIIKYNSGNVLSVLYALERLGINANLTDDVEEIKKADKVIFPGQGEASSAMRYLRERNLDQL---IKDLKQPF 73 79*******************************************************996655...89999*** PP TIGR01855 75 lgiClGmQllfekseEgkevkglglikgkvkkleaekkvPhiGWnevevvkesellkgleeearvYfvHsYave 148 giClG Qll e seE +++++lg+++ kv+k+ + kvPh+GWn+++ ++ + ll+g++++++vY+vHsY +e lcl|FitnessBrowser__Cola:Echvi_2514 74 FGICLGQQLLCEYSEE-NDTECLGVFPVKVRKFPPADKVPHVGWNSLQETQGQ-LLEGINTHDYVYYVHSYFAE 145 ****************.579*************************99988776.******************** PP TIGR01855 149 leeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 ++ e ++ak++y e+f a+++kdn++++Q HPEkS++ G+k+l nfl+ lcl|FitnessBrowser__Cola:Echvi_2514 146 IHP-EFTVAKTHYIEDFSALLQKDNFYAMQAHPEKSSHSGQKILTNFLK 193 **8.8******************************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (194 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 5.62 // [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