Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_038204236.1 Q392_RS07760 aminodeoxychorismate/anthranilate synthase component II
Query= BRENDA::P20576 (201 letters) >NCBI__GCF_000745855.1:WP_038204236.1 Length = 195 Score = 232 bits (592), Expect = 3e-66 Identities = 124/197 (62%), Positives = 146/197 (74%), Gaps = 12/197 (6%) Query: 2 LLMIDNYDSFTYNLVQYFGELKAEVKVVRNDELSVEQIEA---LAPERIVLSPGPCTPNE 58 LLMIDNYDSFTYNLVQYFGEL A+V+ VRNDE++VE I R+V+SPGPC+P E Sbjct: 4 LLMIDNYDSFTYNLVQYFGELGAQVETVRNDEITVEGIGERIDAGVTRLVISPGPCSPAE 63 Query: 59 AGVSLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGVFAGL 118 AGVS+ I FAG+LP+LGVCLGHQSIG AFG ++VRA+Q+MHGK S I GVFAGL Sbjct: 64 AGVSVPAIRAFAGRLPILGVCLGHQSIGAAFGAKIVRAQQLMHGKVSEITTTREGVFAGL 123 Query: 119 ANPLTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRH----KTLNVEGVQFHP 174 TV RYHSL ++R+S PE L +TAWT DG EIMGVRH + +EGVQFHP Sbjct: 124 PERFTVNRYHSLAIERDSRPEELALTAWTD--DG---EIMGVRHTGFAHEVRLEGVQFHP 178 Query: 175 ESILTEQGHELLANFLR 191 ESILTE GH +L NFL+ Sbjct: 179 ESILTEHGHAMLRNFLQ 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: 187 Number of extensions: 10 Number of successful extensions: 3 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: 195 Length adjustment: 20 Effective length of query: 181 Effective length of database: 175 Effective search space: 31675 Effective search space used: 31675 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_038204236.1 Q392_RS07760 (aminodeoxychorismate/anthranilate synthase component II)
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.747256.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-74 235.2 0.0 2.9e-74 235.1 0.0 1.0 1 NCBI__GCF_000745855.1:WP_038204236.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000745855.1:WP_038204236.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 235.1 0.0 2.9e-74 2.9e-74 2 191 .. 4 195 .] 3 195 .] 0.94 Alignments for each domain: == domain 1 score: 235.1 bits; conditional E-value: 2.9e-74 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqei.eallplls.ivisPGPctPdeaaissleliehla 72 +l+idnydsftynlvq++ elga+v rnd++t++ i e++ + ++ +visPGPc+P+ea++s + +i+ +a NCBI__GCF_000745855.1:WP_038204236.1 4 LLMIDNYDSFTYNLVQYFGELGAQVETVRNDEITVEGIgERIDAGVTrLVISPGPCSPAEAGVS-VPAIRAFA 75 89***********************************95677776556****************.******** PP TIGR00566 73 GklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtll 145 G+lPilGvClGhq+++ afGa++vra++++hGkvsei+ ++vfagl + +++ ryhsl +e ++ ++ l NCBI__GCF_000745855.1:WP_038204236.1 76 GRLPILGVCLGHQSIGAAFGAKIVRAQQLMHGKVSEITTTREGVFAGLPER--FTVNRYHSLAIERDSRPEEL 146 ************************************************655..******************** PP TIGR00566 146 evtaleeeeieimairh....rdlpleGvqfhPesilselGkellanflk 191 +ta+++ eim++rh +++ leGvqfhPesil+e+G+++l+nfl+ NCBI__GCF_000745855.1:WP_038204236.1 147 ALTAWTDDG-EIMGVRHtgfaHEVRLEGVQFHPESILTEHGHAMLRNFLQ 195 *******99.******9333346789**********************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (195 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: 11.14 // [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