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_012170734.1 AZC_RS11430 type 1 glutamine amidotransferase
Query= SwissProt::P26922 (196 letters) >NCBI__GCF_000010525.1:WP_012170734.1 Length = 200 Score = 251 bits (641), Expect = 6e-72 Identities = 123/192 (64%), Positives = 143/192 (74%), Gaps = 1/192 (0%) Query: 4 LIDNYDSFTYNLVHYLGELGAELDVRRNDSLTVEEAMALRPEGIVLSPGPCDPDKAGICL 63 LIDNYDSFTYNL HYLGELGA + VRRND++ VE + +P+ IVLSPGPC P++AGIC Sbjct: 6 LIDNYDSFTYNLWHYLGELGATVTVRRNDAMDVEGILGEKPDAIVLSPGPCTPNEAGICC 65 Query: 64 PLIDAAAKAAVPLMGVCLGHQAIGQPFGGTVVRAPVPMHGKVDRMFHQGRGVLKDLPSPF 123 LI A A VP+ GVCLGHQAIGQ FGG VVRAP PMHGK+ + H+GR V + L F Sbjct: 66 DLI-AKASDTVPMFGVCLGHQAIGQVFGGDVVRAPTPMHGKMSEILHEGRSVFRGLNHSF 124 Query: 124 RATRYHSLIVERATLPACLEVTGETEDGLIMALSHRELPIHGVQFHPESIESEHGHKILE 183 +ATRYHSLIV R TLPA LEVT T DGLIM L+HR P+HGVQFHPESI SE+GH ++ Sbjct: 125 QATRYHSLIVARETLPADLEVTAHTADGLIMGLAHRTRPVHGVQFHPESIASENGHALMR 184 Query: 184 NFLNTTRRLETA 195 NFL+ A Sbjct: 185 NFLDIATAFNAA 196 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: 173 Number of extensions: 7 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: 196 Length of database: 200 Length adjustment: 20 Effective length of query: 176 Effective length of database: 180 Effective search space: 31680 Effective search space used: 31680 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_012170734.1 AZC_RS11430 (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.10588.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-73 233.0 0.0 1.4e-73 232.8 0.0 1.0 1 lcl|NCBI__GCF_000010525.1:WP_012170734.1 AZC_RS11430 type 1 glutamine ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010525.1:WP_012170734.1 AZC_RS11430 type 1 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 232.8 0.0 1.4e-73 1.4e-73 2 191 .. 4 188 .. 3 189 .. 0.98 Alignments for each domain: == domain 1 score: 232.8 bits; conditional E-value: 1.4e-73 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelieh 70 v lidnydsftynl ++l elga+v+v+rnd++ ++ i +p+ iv+sPGPctP+ea+i ++li + lcl|NCBI__GCF_000010525.1:WP_012170734.1 4 VTLIDNYDSFTYNLWHYLGELGATVTVRRNDAMDVEGILGEKPDA-IVLSPGPCTPNEAGIC-CDLIAK 70 789*******************************99999999999.***************9.****** PP TIGR00566 71 laGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveae 139 ++ +P++GvClGhqa++q+fG+dvvra + +hGk+sei h+g++vf+gl + ++atryhsl+v e lcl|NCBI__GCF_000010525.1:WP_012170734.1 71 ASDTVPMFGVCLGHQAIGQVFGGDVVRAPTPMHGKMSEILHEGRSVFRGLNHS--FQATRYHSLIVARE 137 **************************************************998..************** PP TIGR00566 140 tldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 tl++ levta + +im++ hr p++GvqfhPesi se+G++l++nfl+ lcl|NCBI__GCF_000010525.1:WP_012170734.1 138 TLPADLEVTAHTADG-LIMGLAHRTRPVHGVQFHPESIASENGHALMRNFLD 188 ***********9999.**********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (200 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.57 // [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