Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate H281DRAFT_01679 H281DRAFT_01679 shikimate dehydrogenase (EC 1.1.1.25)
Query= BRENDA::Q88IJ7 (272 letters) >FitnessBrowser__Burk376:H281DRAFT_01679 Length = 277 Score = 338 bits (868), Expect = 6e-98 Identities = 180/277 (64%), Positives = 211/277 (76%), Gaps = 5/277 (1%) Query: 1 MSDRYAVIGRPINHTKSPLIHGLFAQASNQQLEYGAIEGSLDD---FEAQVLQFRSEGGK 57 MSDRYAVIG PI HTKSPLIHGLFA+ + Q + Y AIEG L+ F+ V F + GGK Sbjct: 1 MSDRYAVIGNPIGHTKSPLIHGLFAEETGQDMTYDAIEGPLEPANAFDDTVRTFIAAGGK 60 Query: 58 GMNITAPFKLRAFELADRRSERAQLARAANALKFEDGRIVAENFDGIGLLRDIEENLGEP 117 GMN+TAPFKL+AF +AD RSERA LA A NA+KFE+GRIVAENFDG+GL+RDIE NL +P Sbjct: 61 GMNVTAPFKLQAFAVADERSERAALAGAVNAMKFENGRIVAENFDGVGLVRDIEINLHQP 120 Query: 118 LRNRRVLLLGAGGAVRGALLPFLQAGPSELVIANRDMAKALALRNEL-DHSRLRISRYEA 176 + +RVL+LGAGGAVRGALLPF+ A P+ LVIANR + KA AL ++ + L Y Sbjct: 121 MAGKRVLVLGAGGAVRGALLPFIAARPARLVIANRHVDKAKALVEQVAADATLVACGYAE 180 Query: 177 LEGQ-SFDIVVNATSASLTADLPPLPADVLGEAALAYELAYGKGLTPFLRLAREQGQARL 235 LE FD+VVNATSASLT PP+P V + AYELAYGKGLTPFLRLAR G + Sbjct: 181 LESMGQFDLVVNATSASLTGQRPPVPPSVFSASGTAYELAYGKGLTPFLRLARHAGVQGV 240 Query: 236 ADGVGMLVEQAAEAFAWWRGVRPDTRAVINQLTIPLE 272 ADGVGMLVEQAAEAFAWWRGVRP T A+I+QLT+PL+ Sbjct: 241 ADGVGMLVEQAAEAFAWWRGVRPRTHAIIDQLTVPLD 277 Lambda K H 0.320 0.137 0.388 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: 237 Number of extensions: 9 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: 272 Length of database: 277 Length adjustment: 25 Effective length of query: 247 Effective length of database: 252 Effective search space: 62244 Effective search space used: 62244 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 H281DRAFT_01679 H281DRAFT_01679 (shikimate dehydrogenase (EC 1.1.1.25))
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.19406.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-78 247.7 0.0 7e-78 247.5 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_01679 H281DRAFT_01679 shikimate dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_01679 H281DRAFT_01679 shikimate dehydrogenase (EC 1.1.1.25) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 247.5 0.0 7e-78 7e-78 3 265 .. 5 272 .. 3 276 .. 0.95 Alignments for each domain: == domain 1 score: 247.5 bits; conditional E-value: 7e-78 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveiee...lekalsgikalglkGvnvTvPfKe 65 ++viGnpi h ksplih +++++g++++Y a+e ++e + +++ ++ a+g kG+nvT PfK lcl|FitnessBrowser__Burk376:H281DRAFT_01679 5 YAVIGNPIGHTKSPLIHGLFAEETGQDMTYDAIEGPLEPanaFDDTVRTFIAAGGKGMNVTAPFKL 70 9*******************************9976543334************************ PP TIGR00507 66 evlellDeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaak 130 ++++++De +e+a+l+gavN +k e+g++v++n Dg+Glv ++e l+++ ++krvl++GAGGa + lcl|FitnessBrowser__Burk376:H281DRAFT_01679 71 QAFAVADERSERAALAGAVNAMKFENGRIVAENFDGVGLVRDIEInLHQPMAGKRVLVLGAGGAVR 136 ********************************************99****9*************** PP TIGR00507 131 avaleLlka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkk.vdliinatsaglsgei 194 +++l++ a + +++iaNR v+ka++l+e++++ + +a +e+e +dl++natsa+l+g+ lcl|FitnessBrowser__Burk376:H281DRAFT_01679 137 GALLPFIAArPARLVIANRHVDKAKALVEQVAADATLVACGYAELESMGqFDLVVNATSASLTGQR 202 ******998799*********************************98877**************** PP TIGR00507 195 deaevkaellkegklvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdve 259 ++v++++++++ ++ l+y ++ tp+l++a++ g + v+dG+gMlv+Qaa +F w+gv p lcl|FitnessBrowser__Burk376:H281DRAFT_01679 203 --PPVPPSVFSASGTAYELAYGKGLTPFLRLARHAGvQGVADGVGMLVEQAAEAFAWWRGVRPRTH 266 ..**********************************889************************999 PP TIGR00507 260 kvfeal 265 ++++l lcl|FitnessBrowser__Burk376:H281DRAFT_01679 267 AIIDQL 272 888776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (277 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: 00:00:00.01 # Mc/sec: 6.79 // [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