Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_029936186.1 N746_RS0109870 type 1 glutamine amidotransferase
Query= BRENDA::P20576 (201 letters) >NCBI__GCF_000711195.1:WP_029936186.1 Length = 197 Score = 306 bits (783), Expect = 2e-88 Identities = 139/195 (71%), Positives = 170/195 (87%) Query: 1 MLLMIDNYDSFTYNLVQYFGELKAEVKVVRNDELSVEQIEALAPERIVLSPGPCTPNEAG 60 MLLMIDNYDSFTYNLVQYFGEL EV V RND++S+EQ+E L P+ +V+SPGPCTPNEAG Sbjct: 1 MLLMIDNYDSFTYNLVQYFGELGQEVLVHRNDQISIEQVETLKPDYLVISPGPCTPNEAG 60 Query: 61 VSLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGVFAGLAN 120 +S+A I+ FAGK+P+LGVCLGHQ+IGQAFGG+++RA+QVMHGKTSP++H + GVF+ L N Sbjct: 61 ISVAAIKHFAGKVPILGVCLGHQAIGQAFGGQIIRAKQVMHGKTSPVYHHNAGVFSDLPN 120 Query: 121 PLTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRHKTLNVEGVQFHPESILTE 180 P+ TRYHSLV+++ SLP+CLEVTAWTQ G +DEIMGVRHK+L +EGVQFHPESILTE Sbjct: 121 PVETTRYHSLVIEQASLPDCLEVTAWTQDEQGEMDEIMGVRHKSLMIEGVQFHPESILTE 180 Query: 181 QGHELLANFLRQQGG 195 QGH++L NFL Q G Sbjct: 181 QGHQMLQNFLNQARG 195 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: 213 Number of extensions: 4 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: 197 Length adjustment: 21 Effective length of query: 180 Effective length of database: 176 Effective search space: 31680 Effective search space used: 31680 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_029936186.1 N746_RS0109870 (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.23680.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-90 285.7 0.3 9.5e-90 285.6 0.3 1.0 1 lcl|NCBI__GCF_000711195.1:WP_029936186.1 N746_RS0109870 type 1 glutamine Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711195.1:WP_029936186.1 N746_RS0109870 type 1 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 285.6 0.3 9.5e-90 9.5e-90 1 191 [. 1 191 [. 1 192 [. 0.98 Alignments for each domain: == domain 1 score: 285.6 bits; conditional E-value: 9.5e-90 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 m+l+idnydsftynlvq++ elg+ev+v+rnd++ ++++e+l+p+ +visPGPctP+ea+is +++i+ lcl|NCBI__GCF_000711195.1:WP_029936186.1 1 MLLMIDNYDSFTYNLVQYFGELGQEVLVHRNDQISIEQVETLKPDY-LVISPGPCTPNEAGIS-VAAIK 67 79********************************************.****************.***** PP TIGR00566 70 hlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvvea 138 h+aGk+PilGvClGhqa++qafG++++ra++v+hGk+s + h++a+vf l nP +++tryhslv+e lcl|NCBI__GCF_000711195.1:WP_029936186.1 68 HFAGKVPILGVCLGHQAIGQAFGGQIIRAKQVMHGKTSPVYHHNAGVFSDLPNP--VETTRYHSLVIEQ 134 ******************************************************..************* PP TIGR00566 139 etldtllevtaleeee....ieimairhrdlpleGvqfhPesilselGkellanflk 191 ++l+++levta+++ e +eim++rh+ l +eGvqfhPesil+e+G+++l+nfl+ lcl|NCBI__GCF_000711195.1:WP_029936186.1 135 ASLPDCLEVTAWTQDEqgemDEIMGVRHKSLMIEGVQFHPESILTEQGHQMLQNFLN 191 ***********9987667889**********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (197 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 5.28 // [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