Align Aminodeoxychorismate/anthranilate synthase component 2; ADC synthase; ADCS; 4-amino-4-deoxychorismate synthase component 2; Aminodeoxychorismate synthase, glutamine amidotransferase component; EC 2.6.1.85; EC 4.1.3.27 (characterized)
to candidate WP_101447279.1 BD749_RS18475 aminodeoxychorismate/anthranilate synthase component II
Query= SwissProt::P28819 (194 letters) >NCBI__GCF_002846395.1:WP_101447279.1 Length = 190 Score = 175 bits (443), Expect = 5e-49 Identities = 81/186 (43%), Positives = 126/186 (67%), Gaps = 3/186 (1%) Query: 1 MILMIDNYDSFTYNLVQYLGELGEELVVKRNDSITIDEIEELSPDFLMISPGPCSPDEAG 60 M+L++DN+DSFTYNLV Y G+LG E+ V RND + +DEI+ L +++SPGP P +AG Sbjct: 1 MLLLLDNFDSFTYNLVDYFGQLGVEMHVLRND-VGLDEIKALPIQGIVLSPGPGEPQKAG 59 Query: 61 ISLEAIKHFAGKIPIFGVCLGHQSIAQVFGGDVVRAERLMHGKTSDIEHDGKTIFEGLKN 120 + +E I+H+ K+P+ G+CLGHQ++ + FG + + + MHGK S+I + +F GL Sbjct: 60 VMMEVIRHYHDKVPMLGICLGHQALGEFFGATLAKGMKPMHGKISEIICEPDPLFNGLPA 119 Query: 121 PLVATRYHSLIVKPETLPSCFTVTAQTKEGEIMAIRHNDLPIEGVQFHPESIMTSFGKEM 180 + RYHSL++ P+ A T EGE+MA RH+ LP+ +QFHPE+ +T++G M Sbjct: 120 RMPVVRYHSLVL--TQWPASILPLAYTAEGELMAFRHSTLPLHALQFHPEAALTTYGLGM 177 Query: 181 LRNFIE 186 L+N+++ Sbjct: 178 LKNWLD 183 Lambda K H 0.320 0.139 0.404 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: 137 Number of extensions: 8 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: 194 Length of database: 190 Length adjustment: 20 Effective length of query: 174 Effective length of database: 170 Effective search space: 29580 Effective search space used: 29580 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: 44 (21.6 bits)
Align candidate WP_101447279.1 BD749_RS18475 (aminodeoxychorismate/anthranilate synthase component II)
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.2283182.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-54 169.4 0.0 4.4e-54 169.2 0.0 1.0 1 NCBI__GCF_002846395.1:WP_101447279.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002846395.1:WP_101447279.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 169.2 0.0 4.4e-54 4.4e-54 1 191 [. 1 183 [. 1 184 [. 0.92 Alignments for each domain: == domain 1 score: 169.2 bits; conditional E-value: 4.4e-54 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaG 73 m+ll+dn+dsftynlv+++ +lg e++v rnd + l+ei+al + iv+sPGP++P++a++ +e+i+h+ NCBI__GCF_002846395.1:WP_101447279.1 1 MLLLLDNFDSFTYNLVDYFGQLGVEMHVLRND-VGLDEIKALPIQG-IVLSPGPGEPQKAGVM-MEVIRHYHD 70 79****************************98.6799***997777.***************8.9******** PP TIGR00566 74 klPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtlle 146 k+P+lG+ClGhqal+ fGa + + k +hGk+sei + +f+gl +++ ryhslv+ ++l+ NCBI__GCF_002846395.1:WP_101447279.1 71 KVPMLGICLGHQALGEFFGATLAKGMKPMHGKISEIICEPDPLFNGLPA--RMPVVRYHSLVLTQW-PASILP 140 ****************************************999999955..59********99743.345666 PP TIGR00566 147 vtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 ++ + e e+ma rh lpl+ +qfhPe+ l+ G +l+n+l+ NCBI__GCF_002846395.1:WP_101447279.1 141 LAYTA-EG-ELMAFRHSTLPLHALQFHPEAALTTYGLGMLKNWLD 183 66555.44.7********************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (190 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: 12.89 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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