Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate Dsui_0170 Dsui_0170 glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase
Query= BRENDA::P20576 (201 letters) >FitnessBrowser__PS:Dsui_0170 Length = 190 Score = 285 bits (728), Expect = 5e-82 Identities = 134/192 (69%), Positives = 161/192 (83%), Gaps = 5/192 (2%) Query: 1 MLLMIDNYDSFTYNLVQYFGELKAEVKVVRNDELSVEQIEALAPERIVLSPGPCTPNEAG 60 MLLMIDNYDSFTYN+VQYFGEL +V+V RND +++ +I L P+ +V+SPGPC P +AG Sbjct: 1 MLLMIDNYDSFTYNIVQYFGELGQDVRVYRNDAITLGEITRLDPDYLVISPGPCAPQQAG 60 Query: 61 VSLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGVFAGLAN 120 VSLA I FAGK+PLLGVCLGHQSIG+AFGG +V A+++MHGKTSP+HH D GVF GL N Sbjct: 61 VSLAAIREFAGKIPLLGVCLGHQSIGEAFGGRIVHAKKLMHGKTSPVHHNDQGVFKGLPN 120 Query: 121 PLTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRHKTLNVEGVQFHPESILTE 180 P+T TRYHSL ++RESLP+CLE+TAWT DG EIMGVRHKTL VEGVQFHPESILTE Sbjct: 121 PVTCTRYHSLAIERESLPDCLEITAWTD--DG---EIMGVRHKTLAVEGVQFHPESILTE 175 Query: 181 QGHELLANFLRQ 192 GH++L NFL++ Sbjct: 176 HGHDMLQNFLKE 187 Lambda K H 0.319 0.137 0.403 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: 207 Number of extensions: 5 Number of successful extensions: 2 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: 201 Length of database: 190 Length adjustment: 20 Effective length of query: 181 Effective length of database: 170 Effective search space: 30770 Effective search space used: 30770 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 (21.7 bits) S2: 44 (21.6 bits)
Align candidate Dsui_0170 Dsui_0170 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase)
to HMM TIGR00566 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase)
# 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/TIGR00566.hmm # target sequence database: /tmp/gapView.7185.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00566 [M=192] Accession: TIGR00566 Description: trpG_papA: glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-87 276.5 0.0 6.4e-87 276.3 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_0170 Dsui_0170 glutamine amidotransfe Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_0170 Dsui_0170 glutamine amidotransferase of anthranilate synthase or aminodeoxychorisma # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 276.3 0.0 6.4e-87 6.4e-87 1 191 [. 1 186 [. 1 187 [. 0.99 Alignments for each domain: == domain 1 score: 276.3 bits; conditional E-value: 6.4e-87 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGklPi 77 m+l+idnydsftyn+vq++ elg++v v rnd++tl ei +l p+ +visPGPc P++a++s l++i+++aGk+P+ lcl|FitnessBrowser__PS:Dsui_0170 1 MLLMIDNYDSFTYNIVQYFGELGQDVRVYRNDAITLGEITRLDPDY-LVISPGPCAPQQAGVS-LAAIREFAGKIPL 75 79********************************************.****************.************* PP TIGR00566 78 lGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtaleeee 154 lGvClGhq+++ afG+ +v+a+k++hGk+s ++hn+++vf+gl nP +++tryhsl +e e+l+++le+ta+++ lcl|FitnessBrowser__PS:Dsui_0170 76 LGVCLGHQSIGEAFGGRIVHAKKLMHGKTSPVHHNDQGVFKGLPNP--VTCTRYHSLAIERESLPDCLEITAWTDDG 150 **********************************************..***************************99 PP TIGR00566 155 ieimairhrdlpleGvqfhPesilselGkellanflk 191 eim++rh+ l++eGvqfhPesil+e+G+ +l+nflk lcl|FitnessBrowser__PS:Dsui_0170 151 -EIMGVRHKTLAVEGVQFHPESILTEHGHDMLQNFLK 186 .**********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (190 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: 4.89 // [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