Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_010961995.1 MCA_RS13680 shikimate dehydrogenase (NADP+)
Query= BRENDA::Q88RQ5 (274 letters) >NCBI__GCF_000008325.1:WP_010961995.1 Length = 279 Score = 288 bits (738), Expect = 7e-83 Identities = 157/272 (57%), Positives = 184/272 (67%), Gaps = 5/272 (1%) Query: 2 DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGG-NVT 60 D+Y VFG+PI HS+SP IH LFA QTGQDL Y P D F C R FF G G N T Sbjct: 5 DRYAVFGHPIEHSQSPRIHALFAAQTGQDLIYTAEDVPPDRFESCVRAFFDGGGRGLNCT 64 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120 +P KE A+ L DS + RA+RA AVNTL ADG++ GDNTDG GL+RDL N G+ LAG Sbjct: 65 IPLKEMAWLLADSRSGRAKRARAVNTLLLRADGSIFGDNTDGIGLLRDLRDNLGLNLAGT 124 Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQ-E 179 +ILILGAGGA RG+L P+LA +P LVIANRTV AE L EF +LGPV GFA L Sbjct: 125 KILILGAGGATRGILAPLLAERPDRLVIANRTVATAETLTVEFGDLGPVEGCGFAALAGR 184 Query: 180 PVDVIINATSASLAGELPPI-ADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDG 238 D+IINAT+ASL+GELPP+ AD L G CYD+ Y EPTPF +W + A DG Sbjct: 185 RFDLIINATAASLSGELPPLPADILAPGGS--CYDLAYAAEPTPFVRWGQEKQAVVSADG 242 Query: 239 LGMLAEQAAEAFFIWRGVRPDTAPVLAELRRQ 270 +GML EQAAEAF +WRGVRP T PV+ L + Sbjct: 243 IGMLVEQAAEAFLLWRGVRPQTRPVIETLEAE 274 Lambda K H 0.319 0.137 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: 286 Number of extensions: 13 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: 274 Length of database: 279 Length adjustment: 25 Effective length of query: 249 Effective length of database: 254 Effective search space: 63246 Effective search space used: 63246 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_010961995.1 MCA_RS13680 (shikimate dehydrogenase (NADP+))
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.20997.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-79 251.0 0.0 6.9e-79 250.8 0.0 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010961995.1 MCA_RS13680 shikimate dehydrogen Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010961995.1 MCA_RS13680 shikimate dehydrogenase (NADP+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 250.8 0.0 6.9e-79 6.9e-79 3 266 .. 7 272 .. 5 275 .. 0.96 Alignments for each domain: == domain 1 score: 250.8 bits; conditional E-value: 6.9e-79 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlell 71 ++v+G+pi+hS sp ih +++q+g++l Y+a +v+++++e+ + +++ g +G+n T+P+Ke + l+ lcl|NCBI__GCF_000008325.1:WP_010961995.1 7 YAVFGHPIEHSQSPRIHALFAAQTGQDLIYTAEDVPPDRFESCVRAFFDGGGRGLNCTIPLKEMAWLLA 75 9******************************************************************** PP TIGR00507 72 DeieesakligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlk 138 D +++ak + avNTl + dg + g+nTDgiGl+ +L+ l ++ ++li+GAGGa+++++ +Ll lcl|NCBI__GCF_000008325.1:WP_010961995.1 76 DSRSGRAKRARAVNTLLlRADGSIFGDNTDGIGLLRDLRDnLGLNLAGTKILILGAGGATRGILAPLLA 144 ****************97789*******************8887778*******************998 PP TIGR00507 139 a.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellke 206 + + +++iaNRtv+ ae l+ ++ lg + + + +++dliinat+a+lsge+ ++++a++l+ lcl|NCBI__GCF_000008325.1:WP_010961995.1 145 ErPDRLVIANRTVATAETLTVEFGDLGPVEGCGFAALAGRRFDLIINATAASLSGEL--PPLPADILAP 211 7699*****************************************************..********** PP TIGR00507 207 gklvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdvekvfealk 266 g ++Dl+y+ tp++++ ++k+ +dG+gMlv+Qaa +F lw+gv p+ v+e+l+ lcl|NCBI__GCF_000008325.1:WP_010961995.1 212 GGSCYDLAYAAEPTPFVRWGQEKQaVVSADGIGMLVEQAAEAFLLWRGVRPQTRPVIETLE 272 *********************99967779************************99999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (279 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: 9.41 // [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