Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate Echvi_0658 Echvi_0658 glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase
Query= SwissProt::P26922 (196 letters) >FitnessBrowser__Cola:Echvi_0658 Length = 196 Score = 139 bits (351), Expect = 3e-38 Identities = 83/189 (43%), Positives = 115/189 (60%), Gaps = 11/189 (5%) Query: 1 MLLLIDNYDSFTYNLVHYLGELGAELDVRRNDSLTVEEAMALRPEGIVLSPGPCDPDKAG 60 MLLLIDN+DSF++ L Y + G +L + RND+ + M + EG+VLSPGP P KAG Sbjct: 1 MLLLIDNFDSFSHILADYFRQAGFDLHIVRNDT-PLAVLMEGKYEGLVLSPGPETPAKAG 59 Query: 61 ICLPLIDAAAKAAVPLMGVCLGHQAIGQPFGGTVVRAPVPMHGKV----DRMFHQGRGVL 116 + + +P++GVCLGHQ IG FG +V P+HGKV R+ H +L Sbjct: 60 NLQEIFEYFHDK-LPVLGVCLGHQCIGTFFGAKLVTGARPVHGKVYSVTKRLDHP---ML 115 Query: 117 KDLPSPFRATRYHSLIVERATLPACLEVTGETEDGLIMALSHRELPIHGVQFHPESIESE 176 LP F TRYHSL E LP CL+ TE G +MA+ H+ LPI G+Q+HPE+ SE Sbjct: 116 NGLPERFLVTRYHSL--ELKDLPDCLQPLLYTEQGALMAMVHQTLPIVGIQYHPEAYLSE 173 Query: 177 HGHKILENF 185 +G ++++N+ Sbjct: 174 YGLQVIQNW 182 Lambda K H 0.321 0.140 0.420 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: 154 Number of extensions: 11 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: 196 Length of database: 196 Length adjustment: 20 Effective length of query: 176 Effective length of database: 176 Effective search space: 30976 Effective search space used: 30976 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 Echvi_0658 Echvi_0658 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate 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.1257.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-47 146.5 0.0 4.7e-47 146.3 0.0 1.0 1 lcl|FitnessBrowser__Cola:Echvi_0658 Echvi_0658 glutamine amidotransf Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_0658 Echvi_0658 glutamine amidotransferase of anthranilate synthase or aminodeoxychor # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 146.3 0.0 4.7e-47 4.7e-47 1 189 [. 1 182 [. 1 185 [. 0.92 Alignments for each domain: == domain 1 score: 146.3 bits; conditional E-value: 4.7e-47 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGk 74 m+llidn+dsf + l +++ + g ++++ rnd+ +e +v+sPGP tP++a+ e++e + k lcl|FitnessBrowser__Cola:Echvi_0658 1 MLLLIDNFDSFSHILADYFRQAGFDLHIVRNDTPLAVLMEGKYEG--LVLSPGPETPAKAGNL-QEIFEYFHDK 71 79******************************9988888875543..7************987.9********* PP TIGR00566 75 lPilGvClGhqalaqafGadvvraekvkhGkvseieh.ngaavfaglfnPdalkatryhslvveaetldtllev 147 lP+lGvClGhq+++ fGa++v+ ++ hGkv+++++ ++ +++gl P+ + +tryhsl ++ l+++l+ lcl|FitnessBrowser__Cola:Echvi_0658 72 LPVLGVCLGHQCIGTFFGAKLVTGARPVHGKVYSVTKrLDHPMLNGL--PERFLVTRYHSLELK--DLPDCLQP 141 **********************************9752688888998..555*********886..79****99 PP TIGR00566 148 taleeeeieimairhrdlpleGvqfhPesilselGkellanf 189 +e+ +ma+ h+ lp+ G+q+hPe+ lse G ++++n+ lcl|FitnessBrowser__Cola:Echvi_0658 142 LLYTEQG-ALMAMVHQTLPIVGIQYHPEAYLSEYGLQVIQNW 182 9998888.9*******************************96 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: 6.78 // [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