Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate Synpcc7942_0400 Synpcc7942_0400 anthranilate synthase, component II
Query= BRENDA::P20576 (201 letters) >FitnessBrowser__SynE:Synpcc7942_0400 Length = 200 Score = 231 bits (588), Expect = 9e-66 Identities = 117/197 (59%), Positives = 147/197 (74%), Gaps = 12/197 (6%) Query: 1 MLLMIDNYDSFTYNLVQYFGELKA------EVKVVRNDELSVEQIEALAPERIVLSPGPC 54 +LL+IDNYDSFTYNLVQY GEL + E+ V RND++ + I AL P+ IV+SPGP Sbjct: 1 VLLVIDNYDSFTYNLVQYLGELASDYAIAQEIVVHRNDQIDLAGIAALKPDAIVISPGPG 60 Query: 55 TPNEAGVSLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGV 114 P +AG+S+A I F P+LGVCLGHQSIGQ +GG++V A ++MHGKTSP+ H D+GV Sbjct: 61 RPEDAGISMAAIAEFGPTTPILGVCLGHQSIGQVYGGQIVSAPELMHGKTSPVLHHDVGV 120 Query: 115 FAGLANPLTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRHKTL-NVEGVQFH 173 F GL NP+T TRYHSLV+ R+S P LEVTAW + DG+ IMGVRH+ +VEGVQFH Sbjct: 121 FQGLDNPITATRYHSLVIDRDSCPADLEVTAWVE--DGT---IMGVRHRQYPHVEGVQFH 175 Query: 174 PESILTEQGHELLANFL 190 PES+LT+ G +LANFL Sbjct: 176 PESVLTQSGKRMLANFL 192 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: 180 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: 200 Length adjustment: 21 Effective length of query: 180 Effective length of database: 179 Effective search space: 32220 Effective search space used: 32220 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 Synpcc7942_0400 Synpcc7942_0400 (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.25535.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-73 232.7 0.0 1.8e-73 232.5 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_0400 Synpcc7942_0400 anthranilate syn Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_0400 Synpcc7942_0400 anthranilate synthase, component II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 232.5 0.0 1.8e-73 1.8e-73 2 191 .. 2 193 .. 1 194 [. 0.97 Alignments for each domain: == domain 1 score: 232.5 bits; conditional E-value: 1.8e-73 TIGR00566 2 vllidnydsftynlvqlleelg......aevvvkrndsltlqeieallpllsivisPGPctPdeaaiss 64 +l+idnydsftynlvq+l el+ +e+vv+rnd++ l+ i al+p+ ivisPGP+ P++a+is lcl|FitnessBrowser__SynE:Synpcc7942_0400 2 LLVIDNYDSFTYNLVQYLGELAsdyaiaQEIVVHRNDQIDLAGIAALKPDA-IVISPGPGRPEDAGIS- 68 799******************99999999**********************.****************. PP TIGR00566 65 leliehlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhs 133 +++i ++ PilGvClGhq+++q+ G+++v a +++hGk+s + h++++vf+gl nP ++atryhs lcl|FitnessBrowser__SynE:Synpcc7942_0400 69 MAAIAEFGPTTPILGVCLGHQSIGQVYGGQIVSAPELMHGKTSPVLHHDVGVFQGLDNP--ITATRYHS 135 89999******************************************************..******** PP TIGR00566 134 lvveaetldtllevtaleeeeieimairhrdlp.leGvqfhPesilselGkellanflk 191 lv++ ++ ++ levta+ e im++rhr++p +eGvqfhPes+l++ Gk++lanfl lcl|FitnessBrowser__SynE:Synpcc7942_0400 136 LVIDRDSCPADLEVTAWVEDG-TIMGVRHRQYPhVEGVQFHPESVLTQSGKRMLANFLA 193 *****************9998.9********9868**********************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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 7.52 // [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