Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate 5208063 Shew_0575 glutamine amidotransferase of anthranilate synthase (RefSeq)
Query= SwissProt::P00901 (198 letters) >FitnessBrowser__PV4:5208063 Length = 195 Score = 239 bits (611), Expect = 2e-68 Identities = 122/195 (62%), Positives = 150/195 (76%), Gaps = 7/195 (3%) Query: 2 LLMMIDNYDSFTYNVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAG 61 +++MIDNYDSFT+N+VQY +LG E+ V RNDE+++A I+AL P R+V+SPGPC+P+EAG Sbjct: 1 MILMIDNYDSFTFNLVQYFQQLGEEIVVRRNDELSLADIQALAPSRLVISPGPCSPNEAG 60 Query: 62 VSIEAILHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVHHRDLGVFTGLNN 121 +S+EAI FAGKLPILGVCLGHQ+I QAFG VVRA++VMHGKTS + H G+FTGLN Sbjct: 61 ISLEAIKAFAGKLPILGVCLGHQAIAQAFGAQVVRAKRVMHGKTSAIAHAGKGLFTGLNQ 120 Query: 122 PLTVTRYHSLVVKRETLPDCLEVTAWTAHEDGSVD--EIMGLRHKTLNIEGVQFHPESIL 179 PLTVTRYHSL+V E LP + AW D V EIM + L + GVQFHPESIL Sbjct: 121 PLTVTRYHSLLV--EQLPKDFTLDAWF---DDPVHGREIMAMSRPELGLFGVQFHPESIL 175 Query: 180 TEQGHELFANFLKQT 194 TEQG EL ANF+KQ+ Sbjct: 176 TEQGLELLANFVKQS 190 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: 162 Number of extensions: 3 Number of successful extensions: 2 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: 195 Length adjustment: 20 Effective length of query: 178 Effective length of database: 175 Effective search space: 31150 Effective search space used: 31150 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 5208063 Shew_0575 (glutamine amidotransferase of anthranilate synthase (RefSeq))
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.2398.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-83 264.9 0.0 2.3e-83 264.7 0.0 1.0 1 lcl|FitnessBrowser__PV4:5208063 Shew_0575 glutamine amidotransfe Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5208063 Shew_0575 glutamine amidotransferase of anthranilate synthase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 264.7 0.0 2.3e-83 2.3e-83 1 191 [. 1 188 [. 1 189 [. 0.97 Alignments for each domain: == domain 1 score: 264.7 bits; conditional E-value: 2.3e-83 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGklPil 78 m+l+idnydsft+nlvq++++lg+e+vv+rnd+l l++i+al+p +visPGPc+P+ea+is le+i+ +aGklPil lcl|FitnessBrowser__PV4:5208063 1 MILMIDNYDSFTFNLVQYFQQLGEEIVVRRNDELSLADIQALAPSR-LVISPGPCSPNEAGIS-LEAIKAFAGKLPIL 76 89********************************************.****************.************** PP TIGR00566 79 GvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtaleeee.. 154 GvClGhqa+aqafGa+vvra++v+hGk+s+i h g+++f+gl +P l++tryhsl ve +l++ +++ a+ + + lcl|FitnessBrowser__PV4:5208063 77 GVCLGHQAIAQAFGAQVVRAKRVMHGKTSAIAHAGKGLFTGLNQP--LTVTRYHSLLVE--QLPKDFTLDAWFDDPvh 150 *********************************************..**********96..79999999999888777 PP TIGR00566 155 .ieimairhrdlpleGvqfhPesilselGkellanflk 191 eima+ + +l l+GvqfhPesil+e+G ellanf+k lcl|FitnessBrowser__PV4:5208063 151 gREIMAMSRPELGLFGVQFHPESILTEQGLELLANFVK 188 89**********************************98 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 4.94 // [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