Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_013707500.1 DESAC_RS12815 type 1 glutamine amidotransferase
Query= BRENDA::P20576 (201 letters) >NCBI__GCF_000195295.1:WP_013707500.1 Length = 239 Score = 181 bits (458), Expect = 1e-50 Identities = 101/194 (52%), Positives = 129/194 (66%), Gaps = 7/194 (3%) Query: 2 LLMIDNYDSFTYNLVQYFGELKAEVKVVRNDELSVEQIEALAPERIVLSPGPCTPNEAGV 61 L++IDNYDSFTYNLVQ F E + EV V R+D++S+ Q+EAL P+ + +SPGP P +AG+ Sbjct: 23 LVIIDNYDSFTYNLVQLFFEFELEVMVFRHDQVSLNQLEALRPDWLCISPGPKAPQDAGL 82 Query: 62 SLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGVFAGLANP 121 S AVI F LP+LGVCLG Q+I + FGG A +HGK I H+ +G+F GL P Sbjct: 83 SKAVIAHFYKTLPILGVCLGMQAINEVFGGVTEPAPVPVHGKRHQIFHQGIGLFKGLPCP 142 Query: 122 LTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRHKTLNVEGVQFHPESILTEQ 181 RYHSL+V+ S + L VTA++ ADG IMG+ H + + GVQFHPES LTE Sbjct: 143 FWAARYHSLMVRPAS--KELMVTAYS--ADG---VIMGLSHWSYPLHGVQFHPESFLTEY 195 Query: 182 GHELLANFLRQQGG 195 G EL ANFLR G Sbjct: 196 GRELAANFLRLAPG 209 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: 162 Number of extensions: 8 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: 201 Length of database: 239 Length adjustment: 22 Effective length of query: 179 Effective length of database: 217 Effective search space: 38843 Effective search space used: 38843 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_013707500.1 DESAC_RS12815 (type 1 glutamine amidotransferase)
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.11789.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-59 184.9 0.0 8.1e-59 184.7 0.0 1.0 1 lcl|NCBI__GCF_000195295.1:WP_013707500.1 DESAC_RS12815 type 1 glutamine a Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195295.1:WP_013707500.1 DESAC_RS12815 type 1 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 184.7 0.0 8.1e-59 8.1e-59 2 191 .. 23 205 .. 22 206 .. 0.96 Alignments for each domain: == domain 1 score: 184.7 bits; conditional E-value: 8.1e-59 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelieh 70 +++idnydsftynlvql+ e ev+v r d++ l+++eal p+ ++isPGP P++a++s ++i h lcl|NCBI__GCF_000195295.1:WP_013707500.1 23 LVIIDNYDSFTYNLVQLFFEFELEVMVFRHDQVSLNQLEALRPDW-LCISPGPKAPQDAGLS-KAVIAH 89 679******************************************.****************.9***** PP TIGR00566 71 laGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveae 139 + lPilGvClG qa+ +fG+ a hGk +i h+g ++f+gl P + a+ryhsl+v+++ lcl|NCBI__GCF_000195295.1:WP_013707500.1 90 FYKTLPILGVCLGMQAINEVFGGVTEPAPVPVHGKRHQIFHQGIGLFKGLPCP--FWAARYHSLMVRPA 156 ***********************99999999**********************..*************9 PP TIGR00566 140 tldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 + + l vta + im++ h +pl+GvqfhPes l+e G+el anfl+ lcl|NCBI__GCF_000195295.1:WP_013707500.1 157 SKE--LMVTAYSADG-VIMGLSHWSYPLHGVQFHPESFLTEYGRELAANFLR 205 866..6688888888.9*********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (239 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: 9.87 // [ok]
This GapMind analysis is from Apr 10 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