Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate WP_011321547.1 AVA_RS24820 anthranilate synthase
Query= curated2:Q57690 (197 letters) >NCBI__GCF_000204075.1:WP_011321547.1 Length = 728 Score = 131 bits (329), Expect = 3e-35 Identities = 80/198 (40%), Positives = 112/198 (56%), Gaps = 12/198 (6%) Query: 4 KKVLVIDNIDSFVWNLVQYVGTLGYKVKLVDNKITLDEIKKINPDRIIISPGPKTPKE-- 61 K++L+ID DSFV L Y+ T G V + + PD +++SPGP P + Sbjct: 526 KRILLIDYEDSFVHTLANYIRTTGATVTTLRHGFAESYFDTERPDLVVLSPGPGRPSDFR 585 Query: 62 AGNCIKIIQEVDIPILGVCLGHQCIVEAFGGEVGRAKRVMHGKASLINHDGEG--IFKDI 119 + + +IPI GVCLG Q IVEAFGGE+G HGK + I+ +F+ + Sbjct: 586 VPQTVAALVGREIPIFGVCLGLQGIVEAFGGELGVLDYPQHGKPARISVTAPDSVLFQHL 645 Query: 120 PNPFYGGRYHSLIA--KEVPKELKITAKSLDDNYIMGVRHKKLPIEGVQFHPESILTESD 177 P F GRYHSL A + +P ELK+ A S +DN IM + H+ LPI VQFHPESI+T + Sbjct: 646 PASFIVGRYHSLFAQPQTIPSELKVIAIS-EDNVIMAIEHQTLPIAAVQFHPESIMTLAG 704 Query: 178 NLKFPDLGLKLIKNFVES 195 ++G +IKN V++ Sbjct: 705 -----EVGQTIIKNVVQT 717 Lambda K H 0.319 0.142 0.421 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: 318 Number of extensions: 16 Number of successful extensions: 4 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: 197 Length of database: 728 Length adjustment: 30 Effective length of query: 167 Effective length of database: 698 Effective search space: 116566 Effective search space used: 116566 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: 49 (23.5 bits)
Align candidate WP_011321547.1 AVA_RS24820 (anthranilate 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.3926756.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-41 127.1 0.0 5.9e-41 126.4 0.0 1.3 1 NCBI__GCF_000204075.1:WP_011321547.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000204075.1:WP_011321547.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 126.4 0.0 5.9e-41 5.9e-41 2 191 .. 528 716 .. 527 717 .. 0.88 Alignments for each domain: == domain 1 score: 126.4 bits; conditional E-value: 5.9e-41 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGk 74 +llid dsf + l +++ ga+v+ + + + ++ p+l +v+sPGP+ P + + + + l G+ NCBI__GCF_000204075.1:WP_011321547.1 528 ILLIDYEDSFVHTLANYIRTTGATVTT-LRHGFAESYFDTERPDL-VVLSPGPGRPSDFRVP--QTVAALVGR 596 8*******************9999875.558999999********.************9988..667777776 PP TIGR00566 75 .lPilGvClGhqalaqafGadvvraekvkhGkvseiehng..aavfaglfnPdalkatryhslvveaetldtl 144 +Pi+GvClG q + afG+++ ++ +hGk i+ + +f+ l P ++ ++ryhsl +++t+++ NCBI__GCF_000204075.1:WP_011321547.1 597 eIPIFGVCLGLQGIVEAFGGELGVLDYPQHGKPARISVTApdSVLFQHL--PASFIVGRYHSLFAQPQTIPSE 667 48******************************99998765004444444..888******************* PP TIGR00566 145 levtaleeeeieimairhrdlpleGvqfhPesils...elGkellanflk 191 l+v a++e + imai h+ lp+ vqfhPesi++ e G+++++n+++ NCBI__GCF_000204075.1:WP_011321547.1 668 LKVIAISEDN-VIMAIEHQTLPIAAVQFHPESIMTlagEVGQTIIKNVVQ 716 *******999.**********************98555788899999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (728 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: 39.68 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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