Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_004322779.1 C665_RS16200 type 1 glutamine amidotransferase
Query= BRENDA::P20576 (201 letters) >NCBI__GCF_000310185.1:WP_004322779.1 Length = 195 Score = 292 bits (748), Expect = 2e-84 Identities = 142/190 (74%), Positives = 165/190 (86%), Gaps = 5/190 (2%) Query: 1 MLLMIDNYDSFTYNLVQYFGELKAEVKVVRNDELSVEQIEALAPERIVLSPGPCTPNEAG 60 MLLMIDNYDSFTYNLVQYFGEL A+VKV RNDE+++EQI LAPE +V+SPGPC+P +AG Sbjct: 1 MLLMIDNYDSFTYNLVQYFGELGAKVKVYRNDEITLEQIGRLAPEHLVISPGPCSPAQAG 60 Query: 61 VSLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGVFAGLAN 120 +S+A I+ FAGKLP+LGVCLGHQSIG+AFGG VV A+++MHGKTSP+HH D GVF GL N Sbjct: 61 ISVAAIKAFAGKLPILGVCLGHQSIGEAFGGRVVHAKRLMHGKTSPVHHIDQGVFRGLPN 120 Query: 121 PLTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRHKTLNVEGVQFHPESILTE 180 PLT TRYHSL ++R SLP+CLEVTAWT+ DG EIMGVRH+TL+VEGVQFHPESILTE Sbjct: 121 PLTCTRYHSLAIERASLPDCLEVTAWTE--DG---EIMGVRHRTLDVEGVQFHPESILTE 175 Query: 181 QGHELLANFL 190 GH LL NFL Sbjct: 176 CGHALLKNFL 185 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: 203 Number of extensions: 4 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: 195 Length adjustment: 20 Effective length of query: 181 Effective length of database: 175 Effective search space: 31675 Effective search space used: 31675 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_004322779.1 C665_RS16200 (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.29286.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-88 281.7 0.0 1.6e-88 281.5 0.0 1.0 1 lcl|NCBI__GCF_000310185.1:WP_004322779.1 C665_RS16200 type 1 glutamine am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000310185.1:WP_004322779.1 C665_RS16200 type 1 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 281.5 0.0 1.6e-88 1.6e-88 1 192 [] 1 187 [. 1 187 [. 0.99 Alignments for each domain: == domain 1 score: 281.5 bits; conditional E-value: 1.6e-88 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 m+l+idnydsftynlvq++ elga+v v rnd++tl++i +l+p++ +visPGPc+P++a+is +++i+ lcl|NCBI__GCF_000310185.1:WP_004322779.1 1 MLLMIDNYDSFTYNLVQYFGELGAKVKVYRNDEITLEQIGRLAPEH-LVISPGPCSPAQAGIS-VAAIK 67 79********************************************.****************.***** PP TIGR00566 70 hlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvvea 138 +aGklPilGvClGhq+++ afG+ vv+a++++hGk+s ++h +++vf+gl nP l++tryhsl +e lcl|NCBI__GCF_000310185.1:WP_004322779.1 68 AFAGKLPILGVCLGHQSIGEAFGGRVVHAKRLMHGKTSPVHHIDQGVFRGLPNP--LTCTRYHSLAIER 134 ******************************************************..************* PP TIGR00566 139 etldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflkr 192 ++l+++levta++e eim++rhr l++eGvqfhPesil+e G++ll+nfl+r lcl|NCBI__GCF_000310185.1:WP_004322779.1 135 ASLPDCLEVTAWTEDG-EIMGVRHRTLDVEGVQFHPESILTECGHALLKNFLDR 187 *************999.**********************************986 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 4.94 // [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