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_035237441.1 Q366_RS06615 type 1 glutamine amidotransferase
Query= SwissProt::P28819 (194 letters) >NCBI__GCF_000745975.1:WP_035237441.1 Length = 189 Score = 214 bits (546), Expect = 6e-61 Identities = 99/183 (54%), Positives = 132/183 (72%) Query: 4 MIDNYDSFTYNLVQYLGELGEELVVKRNDSITIDEIEELSPDFLMISPGPCSPDEAGISL 63 +IDNYDSFT+NLV Y+ G + V RND I+++E+ L D +++SPGP P++AGI L Sbjct: 5 IIDNYDSFTFNLVHYVLHTGAQAEVFRNDKISVEELAGLGFDAIILSPGPGRPEDAGICL 64 Query: 64 EAIKHFAGKIPIFGVCLGHQSIAQVFGGDVVRAERLMHGKTSDIEHDGKTIFEGLKNPLV 123 E ++ +GK+PI GVCLGHQ+IAQ FGG ++ A+ +MHGK S +E DGK IF G+ P Sbjct: 65 ELVQQLSGKVPILGVCLGHQTIAQSFGGTIIHAKAIMHGKISVVEADGKQIFSGINKPFN 124 Query: 124 ATRYHSLIVKPETLPSCFTVTAQTKEGEIMAIRHNDLPIEGVQFHPESIMTSFGKEMLRN 183 RYHSL V+ LP C VTA+T +GEIM IRH + P +GVQFHPES MT+ GK ++RN Sbjct: 125 VMRYHSLAVQESDLPDCLEVTARTLDGEIMGIRHKEHPTQGVQFHPESFMTTVGKRLIRN 184 Query: 184 FIE 186 FI+ Sbjct: 185 FIK 187 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: 137 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: 194 Length of database: 189 Length adjustment: 20 Effective length of query: 174 Effective length of database: 169 Effective search space: 29406 Effective search space used: 29406 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: 44 (21.6 bits)
Align candidate WP_035237441.1 Q366_RS06615 (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.28340.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-70 220.9 0.1 6.9e-70 220.8 0.1 1.0 1 lcl|NCBI__GCF_000745975.1:WP_035237441.1 Q366_RS06615 type 1 glutamine am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745975.1:WP_035237441.1 Q366_RS06615 type 1 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 220.8 0.1 6.9e-70 6.9e-70 4 191 .. 5 187 .. 2 188 .. 0.98 Alignments for each domain: == domain 1 score: 220.8 bits; conditional E-value: 6.9e-70 TIGR00566 4 lidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehla 72 +idnydsft+nlv+++ + ga+ v rnd++ ++e+ l + i++sPGP+ P++a+i lel+++l+ lcl|NCBI__GCF_000745975.1:WP_035237441.1 5 IIDNYDSFTFNLVHYVLHTGAQAEVFRNDKISVEELAGLGFDA-IILSPGPGRPEDAGIC-LELVQQLS 71 7**************************************9999.***************9.******** PP TIGR00566 73 GklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetl 141 Gk+PilGvClGhq++aq+fG+ +++a++++hGk+s +e +g+ +f g+ +P +++ ryhsl v+ l lcl|NCBI__GCF_000745975.1:WP_035237441.1 72 GKVPILGVCLGHQTIAQSFGGTIIHAKAIMHGKISVVEADGKQIFSGINKP--FNVMRYHSLAVQESDL 138 ***************************************************..**************** PP TIGR00566 142 dtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 +++levta + eim+irh++ p +GvqfhPes ++ Gk+l++nf+k lcl|NCBI__GCF_000745975.1:WP_035237441.1 139 PDCLEVTARTLDG-EIMGIRHKEHPTQGVQFHPESFMTTVGKRLIRNFIK 187 ********99988.**********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (189 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: 6.14 // [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