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 Pf6N2E2_1718 Anthranilate synthase, amidotransferase component (EC 4.1.3.27)
Query= SwissProt::P28819 (194 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1718 Length = 194 Score = 181 bits (460), Expect = 6e-51 Identities = 89/190 (46%), Positives = 127/190 (66%), Gaps = 4/190 (2%) Query: 2 ILMIDNYDSFTYNLVQYLGELGEELVVKRND-SITIDEIEELSPDFLMISPGPCSPDEAG 60 + +ID YDSF + + QYL +LG E V+R+D I IE SPDF ++ PGP P + G Sbjct: 3 VFLIDAYDSFVFIISQYLEQLGLETHVERHDVPDLIQRIEAFSPDFCVLGPGPGHPADVG 62 Query: 61 ISLEAIKHFAGKIPIFGVCLGHQSIAQVFGGDVVRAERLMHGKTSDIEHDGKTIFEGLKN 120 +E I+HF G++P+ GVCLGHQ+I FG V RA +MHGK S IE+DGK +++ + Sbjct: 63 Y-IEVIRHFQGRLPLLGVCLGHQAIGLAFGAQVCRAPHVMHGKVSTIENDGKGVYDHTQA 121 Query: 121 PLV-ATRYHSLIVKPETLPSCFTVTAQ-TKEGEIMAIRHNDLPIEGVQFHPESIMTSFGK 178 + ATRYHSL++ + LP C +T++ T +G +M +RH LP+EGVQFHPESI+T G Sbjct: 122 QAIRATRYHSLMISEQPLPDCLEITSRSTDDGYVMGVRHRHLPVEGVQFHPESILTENGL 181 Query: 179 EMLRNFIETY 188 ++ R+FI + Sbjct: 182 DLFRSFIRCH 191 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: 7 Number of successful extensions: 5 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: 194 Length adjustment: 20 Effective length of query: 174 Effective length of database: 174 Effective search space: 30276 Effective search space used: 30276 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 Pf6N2E2_1718 (Anthranilate synthase, amidotransferase component (EC 4.1.3.27))
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.22508.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-66 208.3 0.0 5.2e-66 208.1 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1718 Anthranilate synthase, amidotran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1718 Anthranilate synthase, amidotransferase component (EC 4.1.3.27) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 208.1 0.0 5.2e-66 5.2e-66 2 191 .. 3 189 .. 2 190 .. 0.96 Alignments for each domain: == domain 1 score: 208.1 bits; conditional E-value: 5.2e-66 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrnd.sltlqeieallpllsivisPGPctPdeaaiss 64 v+lid ydsf + + q+le+lg e +v+r d ++ +q iea++p++ v++PGP++P++ + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1718 3 VFLIDAYDSFVFIISQYLEQLGLETHVERHDvPDLIQRIEAFSPDF-CVLGPGPGHPADVGYI- 64 89***************************9945889**********.9**********99976. PP TIGR00566 65 leliehlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalka 128 e+i+h+ G+lP+lGvClGhqa+++afGa+v ra +v+hGkvs ie +g++v+ + a++a lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1718 65 -EVIRHFQGRLPLLGVCLGHQAIGLAFGAQVCRAPHVMHGKVSTIENDGKGVYDHTQAQ-AIRA 126 .***************************************************9887665.9*** PP TIGR00566 129 tryhslvveaetldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 tryhsl++ + l+++le+t+ + + +m++rhr+lp+eGvqfhPesil+e+G l + f++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1718 127 TRYHSLMISEQPLPDCLEITSRSTDDGYVMGVRHRHLPVEGVQFHPESILTENGLDLFRSFIR 189 ***********************************************************9996 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 6.22 // [ok]
This GapMind analysis is from Apr 09 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