Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate HSERO_RS01990 HSERO_RS01990 shikimate 5-dehydrogenase
Query= SwissProt::Q9KVT3 (278 letters) >FitnessBrowser__HerbieS:HSERO_RS01990 Length = 271 Score = 291 bits (744), Expect = 1e-83 Identities = 153/271 (56%), Positives = 193/271 (71%), Gaps = 3/271 (1%) Query: 5 IDQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNV 64 +D+Y V GNPI HSKSP IH FA QT QSM Y VP+ GF A + F +GGRG N+ Sbjct: 1 MDEYVVIGNPIAHSKSPDIHARFAAQTGQSMSYERLLVPLHGFKAAVQVFQRRGGRGANI 60 Query: 65 TVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQ-VLLKG 123 TVPFK EA+ AD+LTERARLAGAVNT K ++G ILGDNTDG GLV D++ L+G Sbjct: 61 TVPFKLEAHALADQLTERARLAGAVNTFK-FEEGCILGDNTDGAGLVTDIMVNAGQALQG 119 Query: 124 ATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQ 183 ILL+GAGGA+RG L PLL Q+PA + V NRT ++AE+LA AAYG V++ F L+ Sbjct: 120 RRILLLGAGGASRGALLPLLQQRPAELVVVNRTASRAEELATQFAAYGPVRSTTFAGLEG 179 Query: 184 SYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAIDGLG 243 ++DVI+N+TSASL +LP + P ++ S ++ YDMMYG+G TVF Q A+QHG A DGLG Sbjct: 180 AFDVIVNATSASLSDDLPPLPPSVYGSETLAYDMMYGRGPTVFMQSAQQHG-AHVRDGLG 238 Query: 244 MLVGQAAESFMLWRGLRPGTKQILRELRKNL 274 MLV QAAE+F WRG+RP T ++ LR+ L Sbjct: 239 MLVEQAAEAFQWWRGVRPATAEVFASLRQQL 269 Lambda K H 0.320 0.135 0.392 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: 211 Number of extensions: 8 Number of successful extensions: 4 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: 278 Length of database: 271 Length adjustment: 25 Effective length of query: 253 Effective length of database: 246 Effective search space: 62238 Effective search space used: 62238 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 HSERO_RS01990 HSERO_RS01990 (shikimate 5-dehydrogenase)
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.30642.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-85 270.4 0.0 7.9e-85 270.2 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS01990 HSERO_RS01990 shikimate 5-dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS01990 HSERO_RS01990 shikimate 5-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 270.2 0.0 7.9e-85 7.9e-85 3 269 .. 4 269 .. 2 270 .. 0.97 Alignments for each domain: == domain 1 score: 270.2 bits; conditional E-value: 7.9e-85 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 + viGnpi+hSksp ih ++++q+g+ + Y ++ v+++ ++ a++ ++ g +G+n+TvPfK e+ +l lcl|FitnessBrowser__HerbieS:HSERO_RS01990 4 YVVIGNPIAHSKSPDIHARFAAQTGQSMSYERLLVPLHGFKAAVQVFQRRGGRGANITVPFKLEAHAL 71 78****************************************************************** PP TIGR00507 71 lDeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLl 137 +D+++e+a+l+gavNT k e+g ++g+nTDg Glv++++ + +++r+l++GAGGa+++++l+Ll lcl|FitnessBrowser__HerbieS:HSERO_RS01990 72 ADQLTERARLAGAVNTFKFEEGCILGDNTDGAGLVTDIMVnAGQALQGRRILLLGAGGASRGALLPLL 139 ***************************************98777777********************* PP TIGR00507 138 ka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaell 204 ++ + e++++NRt ++aeela +++++g + + + +e +d+i+natsa+ls ++ +++++++ lcl|FitnessBrowser__HerbieS:HSERO_RS01990 140 QQrPAELVVVNRTASRAEELATQFAAYGPVRSTTFAGLEG-AFDVIVNATSASLSDDL--PPLPPSVY 204 9989****************************99888875.5****************..******** PP TIGR00507 205 kegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 +++l++D++y + t++++ a+++g++v dGlgMlv+Qaa +F+ w+gv p +vf l+++l lcl|FitnessBrowser__HerbieS:HSERO_RS01990 205 GSETLAYDMMYGRGPTVFMQSAQQHGAHVRDGLGMLVEQAAEAFQWWRGVRPATAEVFASLRQQL 269 **********************************************************9999887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (271 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.81 // [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