Align Anthranilate synthase component II (characterized, see rationale)
to candidate Echvi_2506 Echvi_2506 glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase
Query= uniprot:Q8AAD4_BACTN (188 letters) >FitnessBrowser__Cola:Echvi_2506 Length = 189 Score = 237 bits (604), Expect = 1e-67 Identities = 108/188 (57%), Positives = 149/188 (79%), Gaps = 1/188 (0%) Query: 1 MKILLLDNYDSFTYNLLHAVKELG-ATDVEVVRNDQINLDEVERFDKIILSPGPGIPEEA 59 MKIL+LDNYDSFTYNL++ V+ELG +++V RND+I +++V +DKI+LSPGPG+P +A Sbjct: 1 MKILVLDNYDSFTYNLVYIVRELGYGAEMDVFRNDKIKVEDVAAYDKILLSPGPGVPADA 60 Query: 60 GLLLPIIKRYAPTKSILGVCLGHQAIGEAFGARLENLKEVYHGVQTPISILQKDVLFEGL 119 G++ ++K+YA K ILGVCLGHQAIGEAFG+ L NL EV HGV + + + Q+D+LFEG+ Sbjct: 61 GIMPELLKQYAKEKDILGVCLGHQAIGEAFGSGLNNLTEVVHGVASEVKVFQRDLLFEGV 120 Query: 120 GKEIPVGRYHSWVVSREGFPECLEITAESQEGQIMALRHKTYDVHGIQFHPESVLTPQGK 179 +GRYHSWV+ + LEITA++ +GQIMA+RHK+Y V G+QFHPESVLT GK Sbjct: 121 PDNFKIGRYHSWVIDESTLSDDLEITAKTPDGQIMAVRHKSYKVRGLQFHPESVLTEHGK 180 Query: 180 EIIKNFLN 187 +I++N++N Sbjct: 181 QIVQNWIN 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: 166 Number of extensions: 3 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: 188 Length of database: 189 Length adjustment: 20 Effective length of query: 168 Effective length of database: 169 Effective search space: 28392 Effective search space used: 28392 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 Echvi_2506 Echvi_2506 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase)
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.11833.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-54 170.6 0.0 1.9e-54 170.4 0.0 1.0 1 lcl|FitnessBrowser__Cola:Echvi_2506 Echvi_2506 glutamine amidotransf Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2506 Echvi_2506 glutamine amidotransferase of anthranilate synthase or aminodeoxychor # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 170.4 0.0 1.9e-54 1.9e-54 2 191 .. 3 188 .. 2 189 .] 0.93 Alignments for each domain: == domain 1 score: 170.4 bits; conditional E-value: 1.9e-54 TIGR00566 2 vllidnydsftynlvqlleelg..aevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaG 73 +l++dnydsftynlv + elg ae+ v rnd+++++++ + i++sPGP+ P++a+i el++++a lcl|FitnessBrowser__Cola:Echvi_2506 3 ILVLDNYDSFTYNLVYIVRELGygAEMDVFRNDKIKVEDVA---AYDKILLSPGPGVPADAGIM-PELLKQYAK 72 89******************98879*********9987765...555699*************8.********* PP TIGR00566 74 klPilGvClGhqalaqafGadvvraekvkhGkvseiehnga.avfaglfnPdalkatryhslvveaetldtlle 146 ilGvClGhqa++ afG+ + ++++v hG se++ ++ +f+g+ Pd +k +ryhs v++ tl + le lcl|FitnessBrowser__Cola:Echvi_2506 73 EKDILGVCLGHQAIGEAFGSGLNNLTEVVHGVASEVKVFQRdLLFEGV--PDNFKIGRYHSWVIDESTLSDDLE 144 ************************************976641567776..777********************* PP TIGR00566 147 vtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 +ta++ +ima+rh+ +++ G+qfhPes+l+e+Gk++++n+++ lcl|FitnessBrowser__Cola:Echvi_2506 145 ITAKTPDG-QIMAVRHKSYKVRGLQFHPESVLTEHGKQIVQNWIN 188 ***99998.9********************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (189 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: 6.89 // [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