Align Anthranilate synthase component II (characterized, see rationale)
to candidate 350059 BT0531 anthranilate synthase component II (NCBI ptt file)
Query= uniprot:Q8AAD4_BACTN (188 letters) >FitnessBrowser__Btheta:350059 Length = 188 Score = 380 bits (975), Expect = e-110 Identities = 188/188 (100%), Positives = 188/188 (100%) Query: 1 MKILLLDNYDSFTYNLLHAVKELGATDVEVVRNDQINLDEVERFDKIILSPGPGIPEEAG 60 MKILLLDNYDSFTYNLLHAVKELGATDVEVVRNDQINLDEVERFDKIILSPGPGIPEEAG Sbjct: 1 MKILLLDNYDSFTYNLLHAVKELGATDVEVVRNDQINLDEVERFDKIILSPGPGIPEEAG 60 Query: 61 LLLPIIKRYAPTKSILGVCLGHQAIGEAFGARLENLKEVYHGVQTPISILQKDVLFEGLG 120 LLLPIIKRYAPTKSILGVCLGHQAIGEAFGARLENLKEVYHGVQTPISILQKDVLFEGLG Sbjct: 61 LLLPIIKRYAPTKSILGVCLGHQAIGEAFGARLENLKEVYHGVQTPISILQKDVLFEGLG 120 Query: 121 KEIPVGRYHSWVVSREGFPECLEITAESQEGQIMALRHKTYDVHGIQFHPESVLTPQGKE 180 KEIPVGRYHSWVVSREGFPECLEITAESQEGQIMALRHKTYDVHGIQFHPESVLTPQGKE Sbjct: 121 KEIPVGRYHSWVVSREGFPECLEITAESQEGQIMALRHKTYDVHGIQFHPESVLTPQGKE 180 Query: 181 IIKNFLNE 188 IIKNFLNE Sbjct: 181 IIKNFLNE 188 Lambda K H 0.319 0.141 0.411 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: 282 Number of extensions: 3 Number of successful extensions: 1 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: 188 Length of database: 188 Length adjustment: 20 Effective length of query: 168 Effective length of database: 168 Effective search space: 28224 Effective search space used: 28224 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 350059 BT0531 (anthranilate synthase component II (NCBI ptt file))
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.29786.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-59 186.4 0.0 2.7e-59 186.2 0.0 1.0 1 lcl|FitnessBrowser__Btheta:350059 BT0531 anthranilate synthase com Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:350059 BT0531 anthranilate synthase component II (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 186.2 0.0 2.7e-59 2.7e-59 2 191 .. 3 187 .. 2 188 .] 0.95 Alignments for each domain: == domain 1 score: 186.2 bits; conditional E-value: 2.7e-59 TIGR00566 2 vllidnydsftynlvqlleelg.aevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGklP 76 +ll+dnydsftynl++ ++elg ++v v rnd+++l+e+e++ + i++sPGP+ P+ea++ l +i+++a lcl|FitnessBrowser__Btheta:350059 3 ILLLDNYDSFTYNLLHAVKELGaTDVEVVRNDQINLDEVERFD--K-IILSPGPGIPEEAGLL-LPIIKRYAPTKS 74 9********************9779***************985..4.89*************9.************ PP TIGR00566 77 ilGvClGhqalaqafGadvvraekvkhGkvseiehnga.avfaglfnPdalkatryhslvveaetldtllevtale 151 ilGvClGhqa++ afGa + ++++v hG i+ ++ +f+gl + ++++ryhs vv e+ +++le+ta + lcl|FitnessBrowser__Btheta:350059 75 ILGVCLGHQAIGEAFGARLENLKEVYHGVQTPISILQKdVLFEGLGKE--IPVGRYHSWVVSREGFPECLEITAES 148 *****************************9999876551679***998..99************************ PP TIGR00566 152 eeeieimairhrdlpleGvqfhPesilselGkellanflk 191 +e +ima+rh+ ++++G+qfhPes+l+ +Gke+++nfl+ lcl|FitnessBrowser__Btheta:350059 149 QEG-QIMALRHKTYDVHGIQFHPESVLTPQGKEIIKNFLN 187 999.9*********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (188 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: 8.75 // [ok]
This GapMind analysis is from Apr 09 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