Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate Dsui_0443 Dsui_0443 shikimate 5-dehydrogenase
Query= BRENDA::Q88RQ5 (274 letters) >FitnessBrowser__PS:Dsui_0443 Length = 271 Score = 308 bits (788), Expect = 1e-88 Identities = 170/270 (62%), Positives = 192/270 (71%), Gaps = 4/270 (1%) Query: 2 DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGS-GGNVT 60 D+Y VFGNPIGHSKSPLIH LFA QD+ Y LLAPLD F+ R F G G NVT Sbjct: 3 DRYAVFGNPIGHSKSPLIHSLFAVACAQDMSYEALLAPLDGFAAALRAFADGGGRGANVT 62 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120 VPFKEEAFRL DSLTPRA RAGAVNTL L G + GDNTDGAGLV+DL VN + LAGK Sbjct: 63 VPFKEEAFRLADSLTPRAARAGAVNTLV-LEGGRILGDNTDGAGLVQDLQVNQSLPLAGK 121 Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQ-E 179 IL+LGAGGA RG L P+LA P L IANRT KA LAR+F +LGPV G+ L + Sbjct: 122 AILLLGAGGASRGALAPLLAAGPCRLHIANRTAAKAADLARDFADLGPVSGGGYGELAGQ 181 Query: 180 PVDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGL 239 DV+INATSASLAGELPP+ + G + YDMMYG+ TPF +A GA ++DGL Sbjct: 182 GFDVVINATSASLAGELPPLPPGIFNGG-ALAYDMMYGRGETPFLAFARLEGATHLVDGL 240 Query: 240 GMLAEQAAEAFFIWRGVRPDTAPVLAELRR 269 GML EQAAEAF +WRGVRP TAPVL LR+ Sbjct: 241 GMLVEQAAEAFQLWRGVRPATAPVLDRLRQ 270 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: 310 Number of extensions: 11 Number of successful extensions: 5 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: 271 Length adjustment: 25 Effective length of query: 249 Effective length of database: 246 Effective search space: 61254 Effective search space used: 61254 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 Dsui_0443 Dsui_0443 (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.21540.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-86 274.3 0.0 4.9e-86 274.2 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_0443 Dsui_0443 shikimate 5-dehydrogen Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_0443 Dsui_0443 shikimate 5-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 274.2 0.0 4.9e-86 4.9e-86 3 265 .. 5 268 .. 3 271 .] 0.97 Alignments for each domain: == domain 1 score: 274.2 bits; conditional E-value: 4.9e-86 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeieesak 79 ++v+Gnpi hSksplih ++ +++ Y a+ ++++ + al ++ g +G+nvTvPfKee+++l+D ++++a+ lcl|FitnessBrowser__PS:Dsui_0443 5 YAVFGNPIGHSKSPLIHSLFAVACAQDMSYEALLAPLDGFAAALRAFADGGGRGANVTVPFKEEAFRLADSLTPRAA 81 9**************************************************************************** PP TIGR00507 80 ligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka.dkeviiaNRtvekae 154 +gavNTl+le+g+++g+nTDg Glv++L+ +s + ++k +l++GAGGa+++++ +Ll a ++++ iaNRt +ka lcl|FitnessBrowser__PS:Dsui_0443 82 RAGAVNTLVLEGGRILGDNTDGAGLVQDLQVnQSLPLAGKAILLLGAGGASRGALAPLLAAgPCRLHIANRTAAKAA 158 ******************************98888888*********************9989************** PP TIGR00507 155 elaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegklvvDlvynpletpllkeakkkg. 230 +la ++ lg + e+ + +d++inatsa+l ge+ +++++++++ g+l++D++y +etp+l+ a+ +g lcl|FitnessBrowser__PS:Dsui_0443 159 DLARDFADLGPVSGGGYGELAGQGFDVVINATSASLAGEL--PPLPPGIFNGGALAYDMMYGRGETPFLAFARLEGa 233 ****************************************..**********************************9 PP TIGR00507 231 tkvidGlgMlvaQaalsFelwtgvepdvekvfeal 265 t+ +dGlgMlv+Qaa +F+lw+gv p v ++l lcl|FitnessBrowser__PS:Dsui_0443 234 THLVDGLGMLVEQAAEAFQLWRGVRPATAPVLDRL 268 9*************************998887776 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.80 // [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