Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate BPHYT_RS27375 BPHYT_RS27375 shikimate 5-dehydrogenase
Query= BRENDA::Q88IJ7 (272 letters) >FitnessBrowser__BFirm:BPHYT_RS27375 Length = 277 Score = 352 bits (904), Expect = e-102 Identities = 187/277 (67%), Positives = 217/277 (78%), Gaps = 5/277 (1%) Query: 1 MSDRYAVIGRPINHTKSPLIHGLFAQASNQQLEYGAIEGSLDDFEA---QVLQFRSEGGK 57 M+D+Y+VIG PI HTKSPLIHGLFAQ + Q + Y AIEG L EA V FR+ GGK Sbjct: 1 MTDQYSVIGNPIGHTKSPLIHGLFAQETQQDMSYTAIEGPLSPHEAFAETVNAFRAAGGK 60 Query: 58 GMNITAPFKLRAFELADRRSERAQLARAANALKFEDGRIVAENFDGIGLLRDIEENLGEP 117 GMN+TAPFKL+AF +AD RSERAQLA AANALKFEDGRI AENFDG+GL+RDIE NL P Sbjct: 61 GMNVTAPFKLKAFAMADERSERAQLAGAANALKFEDGRIAAENFDGVGLVRDIEVNLDLP 120 Query: 118 LRNRRVLLLGAGGAVRGALLPFLQAGPSELVIANRDMAKALALRNELD-HSRLRISRYEA 176 + +RVL+LGAGGA+RGALLPFL A P ELVIANRD+AKA AL ++ + L YE Sbjct: 121 MAGKRVLVLGAGGAMRGALLPFLAARPVELVIANRDVAKAEALVAQIGARASLIACGYED 180 Query: 177 LEGQS-FDIVVNATSASLTADLPPLPADVLGEAALAYELAYGKGLTPFLRLAREQGQARL 235 L S FD+VVNATSASLT +LPP+P +V AYELAYGKGLTPFLRLAR G + Sbjct: 181 LAAMSGFDLVVNATSASLTGELPPVPPNVFNPKGAAYELAYGKGLTPFLRLARNAGVLGI 240 Query: 236 ADGVGMLVEQAAEAFAWWRGVRPDTRAVINQLTIPLE 272 ADGVGMLVEQAAEAFAWWRG+RP TR++I+QLT+PL+ Sbjct: 241 ADGVGMLVEQAAEAFAWWRGIRPRTRSLIDQLTVPLD 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: 239 Number of extensions: 12 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 BPHYT_RS27375 BPHYT_RS27375 (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.6368.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-77 244.0 0.0 9.2e-77 243.8 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS27375 BPHYT_RS27375 shikimate 5-dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS27375 BPHYT_RS27375 shikimate 5-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 243.8 0.0 9.2e-77 9.2e-77 2 265 .. 4 272 .. 3 276 .. 0.96 Alignments for each domain: == domain 1 score: 243.8 bits; conditional E-value: 9.2e-77 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafevei...eelekalsgikalglkGvnvTvPfKeevl 68 ++viGnpi h ksplih +++++++++ Y+a+e ++ e++ +++++++a+g kG+nvT PfK +++ lcl|FitnessBrowser__BFirm:BPHYT_RS27375 4 QYSVIGNPIGHTKSPLIHGLFAQETQQDMSYTAIEGPLsphEAFAETVNAFRAAGGKGMNVTAPFKLKAF 73 589******************************99765111569************************** PP TIGR00507 69 ellDeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLl 137 +++De +e+a+l+ga N lk edg++ ++n Dg+Glv ++e l+ + ++krvl++GAGGa ++++l++l lcl|FitnessBrowser__BFirm:BPHYT_RS27375 74 AMADERSERAQLAGAANALKFEDGRIAAENFDGVGLVRDIEVnLDLPMAGKRVLVLGAGGAMRGALLPFL 143 *****************************************99*************************99 PP TIGR00507 138 ka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkk.vdliinatsaglsgeideaevkaellk 205 a + e++iaNR v+kae+l+ ++ + + +a e++ + +dl++natsa+l+ge+ ++v++++++ lcl|FitnessBrowser__BFirm:BPHYT_RS27375 144 AArPVELVIANRDVAKAEALVAQIGARASLIACGYEDLAAMSgFDLVVNATSASLTGEL--PPVPPNVFN 211 9879*********************************999888****************..********* PP TIGR00507 206 egklvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdvekvfeal 265 + +++ l+y ++ tp+l++a++ g ++dG+gMlv+Qaa +F w+g+ p + +++l lcl|FitnessBrowser__BFirm:BPHYT_RS27375 212 PKGAAYELAYGKGLTPFLRLARNAGvLGIADGVGMLVEQAAEAFAWWRGIRPRTRSLIDQL 272 *************************99*************************998888776 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: 6.70 // [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