Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate 17344 b3281 dehydroshikimate reductase, NAD(P)-binding (NCBI)
Query= BRENDA::P15770 (272 letters) >FitnessBrowser__Keio:17344 Length = 272 Score = 541 bits (1394), Expect = e-159 Identities = 272/272 (100%), Positives = 272/272 (100%) Query: 1 METYAVFGNPIAHSKSPFIHQQFAQQLNIEHPYGRVLAPINDFINTLNAFFSAGGKGANV 60 METYAVFGNPIAHSKSPFIHQQFAQQLNIEHPYGRVLAPINDFINTLNAFFSAGGKGANV Sbjct: 1 METYAVFGNPIAHSKSPFIHQQFAQQLNIEHPYGRVLAPINDFINTLNAFFSAGGKGANV 60 Query: 61 TVPFKEEAFARADELTERAALAGAVNTLMRLEDGRLLGDNTDGVGLLSDLERLSFIRPGL 120 TVPFKEEAFARADELTERAALAGAVNTLMRLEDGRLLGDNTDGVGLLSDLERLSFIRPGL Sbjct: 61 TVPFKEEAFARADELTERAALAGAVNTLMRLEDGRLLGDNTDGVGLLSDLERLSFIRPGL 120 Query: 121 RILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHE 180 RILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHE Sbjct: 121 RILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHE 180 Query: 181 FDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGM 240 FDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGM Sbjct: 181 FDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGM 240 Query: 241 LVAQAAHAFLLWHGVLPDVEPVIKQLQEELSA 272 LVAQAAHAFLLWHGVLPDVEPVIKQLQEELSA Sbjct: 241 LVAQAAHAFLLWHGVLPDVEPVIKQLQEELSA 272 Lambda K H 0.321 0.138 0.405 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: 394 Number of extensions: 10 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: 272 Length of database: 272 Length adjustment: 25 Effective length of query: 247 Effective length of database: 247 Effective search space: 61009 Effective search space used: 61009 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: 47 (22.7 bits)
Align candidate 17344 b3281 (dehydroshikimate reductase, NAD(P)-binding (NCBI))
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))
# 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/TIGR00507.hmm # target sequence database: /tmp/gapView.23448.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00507 [M=270] Accession: TIGR00507 Description: aroE: shikimate dehydrogenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-116 373.4 0.0 3.1e-116 373.2 0.0 1.0 1 lcl|FitnessBrowser__Keio:17344 b3281 dehydroshikimate reductase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17344 b3281 dehydroshikimate reductase, NAD(P)-binding (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 373.2 0.0 3.1e-116 3.1e-116 2 269 .. 3 270 .. 2 271 .. 0.99 Alignments for each domain: == domain 1 score: 373.2 bits; conditional E-value: 3.1e-116 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeieesakl 80 +++v+Gnpi+hSksp+ih+++++ql++e++Y ++ ++i+++ ++l++++++g kG+nvTvPfKee+++++De++e+a+l lcl|FitnessBrowser__Keio:17344 3 TYAVFGNPIAHSKSPFIHQQFAQQLNIEHPYGRVLAPINDFINTLNAFFSAGGKGANVTVPFKEEAFARADELTERAAL 81 89***************************************************************************** PP TIGR00507 81 igavNTlk.ledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlkadkeviiaNRtvekaeelae 158 +gavNTl+ ledg+l+g+nTDg+Gl+s+Le+ls++++++r+l+iGAGGa+++v+l+Ll+ d++v+i+NRtv++aeela+ lcl|FitnessBrowser__Keio:17344 82 AGAVNTLMrLEDGRLLGDNTDGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAK 160 ********9********************************************************************** PP TIGR00507 159 rlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegklvvDlvynpletpllkeakkkg.tkvidG 236 ++++g+i+als++e+e +++dliinats+g+sg+i ++++++l++ g++++D++y++++tp+l++++++g ++++dG lcl|FitnessBrowser__Keio:17344 161 LFAHTGSIQALSMDELEGHEFDLIINATSSGISGDI--PAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGsKRNADG 237 ************************************..**********************************899**** PP TIGR00507 237 lgMlvaQaalsFelwtgvepdvekvfealkekl 269 lgMlvaQaa++F lw+gv+pdve v+++l+e+l lcl|FitnessBrowser__Keio:17344 238 LGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEEL 270 ******************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (272 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: 8.82 // [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