Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_015819494.1 TERTU_RS13840 type 1 glutamine amidotransferase
Query= BRENDA::P20576 (201 letters) >NCBI__GCF_000023025.1:WP_015819494.1 Length = 194 Score = 301 bits (771), Expect = 5e-87 Identities = 141/191 (73%), Positives = 163/191 (85%) Query: 1 MLLMIDNYDSFTYNLVQYFGELKAEVKVVRNDELSVEQIEALAPERIVLSPGPCTPNEAG 60 MLLMIDNYDSFTYN+VQY GELKA+V VVRNDELS+++I A PERIV+SPGPCTP EAG Sbjct: 1 MLLMIDNYDSFTYNVVQYLGELKADVHVVRNDELSLDEIIARKPERIVVSPGPCTPTEAG 60 Query: 61 VSLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGVFAGLAN 120 VS+ V++ FAGK+P+ G+CLGHQSIGQAFGG +VRAR+VMHGKTSPIHHK +GVF L Sbjct: 61 VSVEVVQHFAGKIPVFGICLGHQSIGQAFGGNIVRAREVMHGKTSPIHHKGVGVFKDLTT 120 Query: 121 PLTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRHKTLNVEGVQFHPESILTE 180 P TRYHSLV+ + +LP+CLEVTAWT+ DG LDEIMGVRHK VEGVQFHPESIL+E Sbjct: 121 PYLATRYHSLVIDKNTLPDCLEVTAWTETEDGQLDEIMGVRHKDFAVEGVQFHPESILSE 180 Query: 181 QGHELLANFLR 191 GH+LL NFLR Sbjct: 181 HGHQLLENFLR 191 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: 211 Number of extensions: 6 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: 201 Length of database: 194 Length adjustment: 20 Effective length of query: 181 Effective length of database: 174 Effective search space: 31494 Effective search space used: 31494 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: 45 (21.9 bits)
Align candidate WP_015819494.1 TERTU_RS13840 (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.11953.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-87 278.3 0.1 1.8e-87 278.1 0.1 1.0 1 lcl|NCBI__GCF_000023025.1:WP_015819494.1 TERTU_RS13840 type 1 glutamine a Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023025.1:WP_015819494.1 TERTU_RS13840 type 1 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 278.1 0.1 1.8e-87 1.8e-87 1 191 [. 1 191 [. 1 192 [. 0.98 Alignments for each domain: == domain 1 score: 278.1 bits; conditional E-value: 1.8e-87 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 m+l+idnydsftyn+vq+l el a+v+v rnd+l l+ei a +p+ iv+sPGPctP ea++s +e+++ lcl|NCBI__GCF_000023025.1:WP_015819494.1 1 MLLMIDNYDSFTYNVVQYLGELKADVHVVRNDELSLDEIIARKPER-IVVSPGPCTPTEAGVS-VEVVQ 67 79*******************************************9.****************.***** PP TIGR00566 70 hlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvvea 138 h+aGk+P++G+ClGhq+++qafG+++vra++v+hGk+s i+h+g++vf+ l+ P + atryhslv++ lcl|NCBI__GCF_000023025.1:WP_015819494.1 68 HFAGKIPVFGICLGHQSIGQAFGGNIVRAREVMHGKTSPIHHKGVGVFKDLTTP--YLATRYHSLVIDK 134 ******************************************************..9************ PP TIGR00566 139 etldtllevtaleeee....ieimairhrdlpleGvqfhPesilselGkellanflk 191 +tl+++levta++e+e +eim++rh+d ++eGvqfhPesilse+G++ll+nfl+ lcl|NCBI__GCF_000023025.1:WP_015819494.1 135 NTLPDCLEVTAWTETEdgqlDEIMGVRHKDFAVEGVQFHPESILSEHGHQLLENFLR 191 ************998878889**********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.05 // [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