Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate 5211315 Shew_3727 shikimate 5-dehydrogenase (RefSeq)
Query= SwissProt::Q9KVT3 (278 letters) >FitnessBrowser__PV4:5211315 Length = 304 Score = 311 bits (797), Expect = 1e-89 Identities = 156/275 (56%), Positives = 196/275 (71%), Gaps = 1/275 (0%) Query: 1 MASQI-DQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGG 59 M Q+ D+YAVFG+PI HSKSP IH FA+ T +S+ Y A P+DGF E+ + FF GG Sbjct: 26 MTQQVQDRYAVFGHPIGHSKSPAIHQAFAKSTGESLQYEAILAPLDGFAESLRAFFEHGG 85 Query: 60 RGCNVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQV 119 +G NVT+PFKE+AY D L + A+LAGAVNTL +L DG I GDNTDG GLV DL Sbjct: 86 KGANVTLPFKEQAYALCDCLGDEAKLAGAVNTLTRLADGRIKGDNTDGLGLVADLERHLG 145 Query: 120 LLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFE 179 L G ++LLIGAGGAARG + PLL+ S+T+ NRT +KAEQLAE AYG+VKA + Sbjct: 146 SLCGKSVLLIGAGGAARGAILPLLNAGIDSLTIHNRTHSKAEQLAEAFKAYGQVKASTLD 205 Query: 180 QLKQSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAI 239 +L S+D++INSTSASL GELP++ I ++ SVCYDMMYG+ T FN WA G +Q I Sbjct: 206 ELTHSFDIVINSTSASLSGELPSLPKAIIAAHSVCYDMMYGRELTAFNHWALDQGASQTI 265 Query: 240 DGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNL 274 DGLGMLVGQAA+SF +WRG+ P + +L +LR L Sbjct: 266 DGLGMLVGQAAKSFAIWRGVEPAVEPVLAKLRSEL 300 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: 250 Number of extensions: 7 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: 278 Length of database: 304 Length adjustment: 26 Effective length of query: 252 Effective length of database: 278 Effective search space: 70056 Effective search space used: 70056 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: 48 (23.1 bits)
Align candidate 5211315 Shew_3727 (shikimate 5-dehydrogenase (RefSeq))
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.29367.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-91 291.1 0.0 4e-91 290.9 0.0 1.0 1 lcl|FitnessBrowser__PV4:5211315 Shew_3727 shikimate 5-dehydrogen Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5211315 Shew_3727 shikimate 5-dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 290.9 0.0 4e-91 4e-91 3 269 .. 34 300 .. 32 301 .. 0.97 Alignments for each domain: == domain 1 score: 290.9 bits; conditional E-value: 4e-91 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeieesakl 80 ++v+G+pi hSksp+ih+a++k +g l+Y a+ ++++ + + l ++++ g kG+nvT+PfKe++++l+D + ++akl lcl|FitnessBrowser__PV4:5211315 34 YAVFGHPIGHSKSPAIHQAFAKSTGESLQYEAILAPLDGFAESLRAFFEHGGKGANVTLPFKEQAYALCDCLGDEAKL 111 9***************************************************************************** PP TIGR00507 81 igavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka.dkeviiaNRtvekaee 155 +gavNTl+ l dg++ g+nTDg+Glv++Le+ l l +k+vl+iGAGGaa++++l+Ll+a +++i NRt +kae+ lcl|FitnessBrowser__PV4:5211315 112 AGAVNTLTrLADGRIKGDNTDGLGLVADLERhLGSLC-GKSVLLIGAGGAARGAILPLLNAgIDSLTIHNRTHSKAEQ 188 *******99**********************999999.***********************4568************* PP TIGR00507 156 laerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegklvvDlvynpletpllkeakkkg.tk 232 lae+++++g+++a l+e+ +++d++in+tsa+lsge+ +++++ ++++ ++++D++y t++ ++a ++g ++ lcl|FitnessBrowser__PV4:5211315 189 LAEAFKAYGQVKASTLDEL-THSFDIVINSTSASLSGEL--PSLPKAIIAAHSVCYDMMYGRELTAFNHWALDQGaSQ 263 ************9998887.689****************..**********************************99* PP TIGR00507 233 vidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 +idGlgMlv Qaa+sF +w+gvep ve v +l+++l lcl|FitnessBrowser__PV4:5211315 264 TIDGLGMLVGQAAKSFAIWRGVEPAVEPVLAKLRSEL 300 ******************************9999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (304 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: 10.31 // [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