Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate WP_034995003.1 DL88_RS09215 type 1 glutamine amidotransferase
Query= SwissProt::P26922 (196 letters) >NCBI__GCF_000745425.1:WP_034995003.1 Length = 199 Score = 236 bits (602), Expect = 2e-67 Identities = 115/186 (61%), Positives = 142/186 (76%), Gaps = 2/186 (1%) Query: 2 LLLIDNYDSFTYNLVHYLGELGAELDVRRNDSLTVEEAMALRPEGIVLSPGPCDPDKAGI 61 +LLIDNYDSFT+NLVH +G LGA +DV RND +T E +A RP+ IVLSPGPC P +AGI Sbjct: 4 VLLIDNYDSFTWNLVHGIGALGARVDVHRNDKITPSEVLAARPDAIVLSPGPCTPREAGI 63 Query: 62 CLPLIDAAAKAAVPLMGVCLGHQAIGQPFGGTVVRAPVPMHGKVDRMFHQGRGVLKDLPS 121 CL LI A + +P+ GVCLGHQAIG+ FGG VVRAP P+HGK+ + HQG+ + + + Sbjct: 64 CLDLIKTAG-SQIPIFGVCLGHQAIGEVFGGNVVRAPEPVHGKLAVIDHQGQSLFRGING 122 Query: 122 PFRATRYHSLIVERATLPACLEVTGETEDGLIMALSHRELPIHGVQFHPESIESEHGHKI 181 PF+A RYHSLIV+R +LP L +T ET+ GLIM LSH+ LPIHGVQFHPESI SE G +I Sbjct: 123 PFKAARYHSLIVDRESLPQDLSITAETQ-GLIMGLSHKSLPIHGVQFHPESIASEQGARI 181 Query: 182 LENFLN 187 NFL+ Sbjct: 182 FANFLD 187 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: 192 Number of extensions: 7 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: 196 Length of database: 199 Length adjustment: 20 Effective length of query: 176 Effective length of database: 179 Effective search space: 31504 Effective search space used: 31504 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 WP_034995003.1 DL88_RS09215 (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.31146.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-69 220.1 0.0 1.3e-69 219.9 0.0 1.0 1 lcl|NCBI__GCF_000745425.1:WP_034995003.1 DL88_RS09215 type 1 glutamine am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745425.1:WP_034995003.1 DL88_RS09215 type 1 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 219.9 0.0 1.3e-69 1.3e-69 1 191 [. 3 187 .. 3 188 .. 0.97 Alignments for each domain: == domain 1 score: 219.9 bits; conditional E-value: 1.3e-69 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 +vllidnydsft+nlv+ + lga v v+rnd++t +e+ a p+ iv+sPGPctP ea+i l+li+ lcl|NCBI__GCF_000745425.1:WP_034995003.1 3 SVLLIDNYDSFTWNLVHGIGALGARVDVHRNDKITPSEVLAARPDA-IVLSPGPCTPREAGIC-LDLIK 69 59*******************************************9.***************9.***** PP TIGR00566 70 hlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvvea 138 + ++Pi+GvClGhqa++ +fG++vvra + hGk+ i+h+g+++f+g+ P +ka+ryhsl+v+ lcl|NCBI__GCF_000745425.1:WP_034995003.1 70 TAGSQIPIFGVCLGHQAIGEVFGGNVVRAPEPVHGKLAVIDHQGQSLFRGINGP--FKAARYHSLIVDR 136 ******************************************************..************* PP TIGR00566 139 etldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 e+l++ l++ta ++ +im++ h+ lp++GvqfhPesi se+G+++ anfl+ lcl|NCBI__GCF_000745425.1:WP_034995003.1 137 ESLPQDLSITAETQ--GLIMGLSHKSLPIHGVQFHPESIASEQGARIFANFLD 187 *****999988655..47*********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (199 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: 7.69 // [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