Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_026608556.1 METAC_RS0121195 type 1 glutamine amidotransferase
Query= BRENDA::P20576 (201 letters) >NCBI__GCF_000427445.1:WP_026608556.1 Length = 187 Score = 198 bits (504), Expect = 4e-56 Identities = 102/190 (53%), Positives = 129/190 (67%), Gaps = 9/190 (4%) Query: 1 MLLMIDNYDSFTYNLVQYFGELKAEVKVVRNDELSVEQIEALAPERIVLSPGPCTPNEAG 60 M+L++DNYDSF + + Y EL A VVRND ++ PE IV+SPGPCTPNEAG Sbjct: 1 MILVVDNYDSFVHTVAGYLSELGATPVVVRNDAPLPDE----TPEAIVISPGPCTPNEAG 56 Query: 61 VSLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGVFAGLAN 120 VS+A+I ++G+ P+LG+CLGHQ IGQ FGG V RA + MHG+ S + H LG+ GL + Sbjct: 57 VSMALIREYSGRAPILGICLGHQCIGQVFGGTVRRALRPMHGEASLVRHDALGILEGLPS 116 Query: 121 PLTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRHKTLNVEGVQFHPESILTE 180 PL V RYHSL+V E L TAW+Q DG EIM ++H+ GVQFHPESILTE Sbjct: 117 PLNVGRYHSLIVDLEGGEASLAATAWSQ--DG---EIMALQHREHPTFGVQFHPESILTE 171 Query: 181 QGHELLANFL 190 GH++L NFL Sbjct: 172 HGHQILRNFL 181 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: 172 Number of extensions: 6 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: 201 Length of database: 187 Length adjustment: 20 Effective length of query: 181 Effective length of database: 167 Effective search space: 30227 Effective search space used: 30227 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: 44 (21.6 bits)
Align candidate WP_026608556.1 METAC_RS0121195 (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.4068.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-66 209.1 0.0 3.1e-66 208.9 0.0 1.0 1 lcl|NCBI__GCF_000427445.1:WP_026608556.1 METAC_RS0121195 type 1 glutamine Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_026608556.1 METAC_RS0121195 type 1 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 208.9 0.0 3.1e-66 3.1e-66 1 191 [. 1 182 [. 1 183 [. 0.97 Alignments for each domain: == domain 1 score: 208.9 bits; conditional E-value: 3.1e-66 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 m+l++dnydsf + + +l+elga+ vv rnd+ +e +p+ ivisPGPctP+ea++s ++li+ lcl|NCBI__GCF_000427445.1:WP_026608556.1 1 MILVVDNYDSFVHTVAGYLSELGATPVVVRNDAPLPDE----TPEA-IVISPGPCTPNEAGVS-MALIR 63 79*****************************9987766....6777.****************.99*** PP TIGR00566 70 hlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvvea 138 +++G+ PilG+ClGhq+++q+fG+ v ra + +hG+ s ++h+ ++++gl +P l+++ryhsl+v+ lcl|NCBI__GCF_000427445.1:WP_026608556.1 64 EYSGRAPILGICLGHQCIGQVFGGTVRRALRPMHGEASLVRHDALGILEGLPSP--LNVGRYHSLIVDL 130 ******************************************************..************* PP TIGR00566 139 etldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 e+ ++ l ta+++ eima++hr+ p +GvqfhPesil+e+G+++l+nfl lcl|NCBI__GCF_000427445.1:WP_026608556.1 131 EGGEASLAATAWSQDG-EIMALQHREHPTFGVQFHPESILTEHGHQILRNFLG 182 *************999.**********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (187 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: 5.89 // [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