Align Aminodeoxychorismate/anthranilate synthase component 2; ADC synthase; ADCS; 4-amino-4-deoxychorismate synthase component 2; Aminodeoxychorismate synthase, glutamine amidotransferase component; EC 2.6.1.85; EC 4.1.3.27 (characterized)
to candidate WP_028950797.1 Q385_RS0105980 type 1 glutamine amidotransferase
Query= SwissProt::P28819 (194 letters) >NCBI__GCF_000619805.1:WP_028950797.1 Length = 198 Score = 238 bits (608), Expect = 4e-68 Identities = 113/186 (60%), Positives = 144/186 (77%), Gaps = 1/186 (0%) Query: 1 MILMIDNYDSFTYNLVQYLGELGEELVVKRNDSITIDEIEELSP-DFLMISPGPCSPDEA 59 MILMIDNYDSFTYN+VQY ELG+E++VKRND ITI++I+ + D ++ISPGPC+P+EA Sbjct: 1 MILMIDNYDSFTYNIVQYFYELGQEVLVKRNDEITIEDIKRMDNIDAIVISPGPCTPNEA 60 Query: 60 GISLEAIKHFAGKIPIFGVCLGHQSIAQVFGGDVVRAERLMHGKTSDIEHDGKTIFEGLK 119 GIS++ IK F G PI GVCLGHQSI Q FGG +V+A+ LMHGKTS I H+ K +FEG+ Sbjct: 61 GISVDVIKEFKGVYPILGVCLGHQSIGQAFGGKIVKAKCLMHGKTSKIYHNEKGLFEGIP 120 Query: 120 NPLVATRYHSLIVKPETLPSCFTVTAQTKEGEIMAIRHNDLPIEGVQFHPESIMTSFGKE 179 NP A RYHSL++ TLP +TA++ +GEIMAI H PI GVQFHPESI+T +G + Sbjct: 121 NPFNAVRYHSLVIDESTLPEDIEITARSDDGEIMAIEHKKYPIWGVQFHPESILTEYGLK 180 Query: 180 MLRNFI 185 +L NF+ Sbjct: 181 LLENFV 186 Lambda K H 0.320 0.139 0.404 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: 168 Number of extensions: 6 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: 194 Length of database: 198 Length adjustment: 20 Effective length of query: 174 Effective length of database: 178 Effective search space: 30972 Effective search space used: 30972 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 (21.8 bits) S2: 45 (21.9 bits)
Align candidate WP_028950797.1 Q385_RS0105980 (type 1 glutamine amidotransferase)
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.26088.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-83 265.6 0.0 1.4e-83 265.4 0.0 1.0 1 lcl|NCBI__GCF_000619805.1:WP_028950797.1 Q385_RS0105980 type 1 glutamine Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000619805.1:WP_028950797.1 Q385_RS0105980 type 1 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 265.4 0.0 1.4e-83 1.4e-83 1 191 [. 1 187 [. 1 188 [. 0.99 Alignments for each domain: == domain 1 score: 265.4 bits; conditional E-value: 1.4e-83 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 m+l+idnydsftyn+vq++ elg+ev+vkrnd++t+++i+++ +ivisPGPctP+ea+is +++i+ lcl|NCBI__GCF_000619805.1:WP_028950797.1 1 MILMIDNYDSFTYNIVQYFYELGQEVLVKRNDEITIEDIKRMDNIDAIVISPGPCTPNEAGIS-VDVIK 68 89*************************************************************.***** PP TIGR00566 70 hlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvvea 138 ++ G PilGvClGhq+++qafG+++v+a+ ++hGk+s+i hn++++f+g+ nP ++a ryhslv++ lcl|NCBI__GCF_000619805.1:WP_028950797.1 69 EFKGVYPILGVCLGHQSIGQAFGGKIVKAKCLMHGKTSKIYHNEKGLFEGIPNP--FNAVRYHSLVIDE 135 ******************************************************..************* PP TIGR00566 139 etldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 tl++ +e+ta ++ eimai h+++p+ GvqfhPesil+e G +ll+nf++ lcl|NCBI__GCF_000619805.1:WP_028950797.1 136 STLPEDIEITARSDDG-EIMAIEHKKYPIWGVQFHPESILTEYGLKLLENFVH 187 **************99.**********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (198 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: 6.27 // [ok]
This GapMind analysis is from Apr 10 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