Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate Ac3H11_769 Anthranilate synthase, amidotransferase component (EC 4.1.3.27) @ Para-aminobenzoate synthase, amidotransferase component (EC 2.6.1.85)
Query= SwissProt::P00901 (198 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_769 Length = 196 Score = 265 bits (677), Expect = 4e-76 Identities = 130/195 (66%), Positives = 157/195 (80%), Gaps = 9/195 (4%) Query: 3 LMMIDNYDSFTYNVVQYLGELGAEVKVIRNDEMTIAQIEAL----NPERIVVSPGPCTPS 58 L+M+DNYDSFTYN+VQY GELGAEV+V RNDE+T+A+IEA +R+V+SPGPC+P+ Sbjct: 5 LLMVDNYDSFTYNIVQYFGELGAEVEVFRNDEITVAEIEARLDAGQLDRLVISPGPCSPA 64 Query: 59 EAGVSIEAILHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVHHRDLGVFTG 118 EAG+S+ AI HFAGKLPILGVCLGHQSIG AFGG+++RA+++MHGKTS + GVF G Sbjct: 65 EAGISVAAIQHFAGKLPILGVCLGHQSIGAAFGGNIIRAQELMHGKTSVITTTQKGVFAG 124 Query: 119 LNNPLTVTRYHSLVVKRETLPDCLEVTAWTAHEDGSVDEIMGLRHKTLNIEGVQFHPESI 178 L TV RYHSL ++R T P+ LEVTAWT EDG EIMG+RHKTL IEGVQFHPESI Sbjct: 125 LPEKFTVNRYHSLAIERATCPEVLEVTAWT--EDG---EIMGVRHKTLPIEGVQFHPESI 179 Query: 179 LTEQGHELFANFLKQ 193 LTE GH + NFL+Q Sbjct: 180 LTEHGHAMLKNFLEQ 194 Lambda K H 0.320 0.138 0.411 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: 5 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: 198 Length of database: 196 Length adjustment: 20 Effective length of query: 178 Effective length of database: 176 Effective search space: 31328 Effective search space used: 31328 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: 45 (21.9 bits)
Align candidate Ac3H11_769 (Anthranilate synthase, amidotransferase component (EC 4.1.3.27) @ Para-aminobenzoate synthase, amidotransferase component (EC 2.6.1.85))
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.32506.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-82 259.4 0.0 1.1e-81 259.2 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_769 Anthranilate synthase, amidotran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_769 Anthranilate synthase, amidotransferase component (EC 4.1.3.27) @ Par # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 259.2 0.0 1.1e-81 1.1e-81 2 191 .. 5 193 .. 4 194 .. 0.95 Alignments for each domain: == domain 1 score: 259.2 bits; conditional E-value: 1.1e-81 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallplls...ivisPGPctPdeaa 61 +l++dnydsftyn+vq++ elgaev v rnd++t++eiea l + +visPGPc+P+ea+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_769 5 LLMVDNYDSFTYNIVQYFGELGAEVEVFRNDEITVAEIEARLDAGQldrLVISPGPCSPAEAG 67 79*************************************8654433357************** PP TIGR00566 62 issleliehlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPd 124 is +++i+h+aGklPilGvClGhq+++ afG++++ra++++hGk+s i+ +++vfagl + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_769 68 IS-VAAIQHFAGKLPILGVCLGHQSIGAAFGGNIIRAQELMHGKTSVITTTQKGVFAGLPEK- 128 **.********************************************************555. PP TIGR00566 125 alkatryhslvveaetldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkella 187 +++ ryhsl +e +t +++levta++e eim++rh+ lp+eGvqfhPesil+e+G+++l+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_769 129 -FTVNRYHSLAIERATCPEVLEVTAWTEDG-EIMGVRHKTLPIEGVQFHPESILTEHGHAMLK 189 .**************************999.******************************** PP TIGR00566 188 nflk 191 nfl+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_769 190 NFLE 193 **97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (196 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: 6.58 // [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