Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_014149884.1 MEALZ_RS16965 shikimate dehydrogenase
Query= SwissProt::Q9KVT3 (278 letters) >NCBI__GCF_000968535.2:WP_014149884.1 Length = 275 Score = 285 bits (729), Expect = 8e-82 Identities = 147/270 (54%), Positives = 187/270 (69%), Gaps = 2/270 (0%) Query: 3 SQIDQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGC 62 +QIDQYAVFG+PI HSKSP IH +FA QT Q +IYTAQ V D F A FF GG+G Sbjct: 2 TQIDQYAVFGSPIKHSKSPTIHRIFAEQTGQELIYTAQEVTADRFESAVTEFFRLGGQGL 61 Query: 63 NVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLA-QQVLL 121 N TVP KE A+RFADR TERA A AVNTL DG ILGDNTDG GLV DL+ +V L Sbjct: 62 NCTVPLKELAWRFADRKTERAESAKAVNTLTLQADGSILGDNTDGIGLVTDLIVNHEVTL 121 Query: 122 KGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQL 181 G +L++GAGGA+RG+L PL +QQPA + V NRT +KA LA+ A G++ F++L Sbjct: 122 NGKKLLILGAGGASRGILSPLFEQQPAWVLVANRTASKAVNLADEFADRGDINGCGFDEL 181 Query: 182 K-QSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAID 240 S+DVI+N+TSASL +LP + + + VCYD+ YG T F +W+ HG A ++D Sbjct: 182 AGLSFDVILNATSASLSNDLPPLPEGLLAPNGVCYDLAYGNEPTAFVRWSISHGAASSLD 241 Query: 241 GLGMLVGQAAESFMLWRGLRPGTKQILREL 270 GLGMLV QAAE+F++WRG+RP T +++ L Sbjct: 242 GLGMLVEQAAEAFLIWRGIRPDTAPVIKLL 271 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: 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: 278 Length of database: 275 Length adjustment: 25 Effective length of query: 253 Effective length of database: 250 Effective search space: 63250 Effective search space used: 63250 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 WP_014149884.1 MEALZ_RS16965 (shikimate 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.9700.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-83 265.9 0.0 1.9e-83 265.7 0.0 1.0 1 lcl|NCBI__GCF_000968535.2:WP_014149884.1 MEALZ_RS16965 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000968535.2:WP_014149884.1 MEALZ_RS16965 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 265.7 0.0 1.9e-83 1.9e-83 2 265 .. 6 271 .. 5 274 .. 0.96 Alignments for each domain: == domain 1 score: 265.7 bits; conditional E-value: 1.9e-83 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 ++v+G pikhSksp ih +++q+g+el Y+a ev+ +++e+a+++++ lg +G+n TvP+Ke + ++ lcl|NCBI__GCF_000968535.2:WP_014149884.1 6 QYAVFGSPIKHSKSPTIHRIFAEQTGQELIYTAQEVTADRFESAVTEFFRLGGQGLNCTVPLKELAWRF 74 69******************************************************************* PP TIGR00507 71 lDeieesakligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLl 137 +D+ +e+a+ ++avNTl+ dg ++g+nTDgiGlv++L + ++k++li+GAGGa+++++ +L lcl|NCBI__GCF_000968535.2:WP_014149884.1 75 ADRKTERAESAKAVNTLTlQADGSILGDNTDGIGLVTDLIVnHEVTLNGKKLLILGAGGASRGILSPLF 143 ******************55799****************9855555679******************99 PP TIGR00507 138 ka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellk 205 ++ + v++aNRt +ka +la++++ g+i +e+ ++d+i+natsa+ls+++ ++++++ll+ lcl|NCBI__GCF_000968535.2:WP_014149884.1 144 EQqPAWVLVANRTASKAVNLADEFADRGDINGCGFDELAGLSFDVILNATSASLSNDL--PPLPEGLLA 210 885788****************************************************..********* PP TIGR00507 206 egklvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdvekvfeal 265 + +++Dl+y t++++++ ++g ++ +dGlgMlv+Qaa +F +w+g+ pd v++ l lcl|NCBI__GCF_000968535.2:WP_014149884.1 211 PNGVCYDLAYGNEPTAFVRWSISHGaASSLDGLGMLVEQAAEAFLIWRGIRPDTAPVIKLL 271 *************************999*************************99998866 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (275 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.41 // [ok]
This GapMind analysis is from Apr 10 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