Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_011882038.1 shikimate dehydrogenase
Query= BRENDA::Q88IJ7 (272 letters) >NCBI__GCF_000016205.1:WP_011882038.1 Length = 277 Score = 334 bits (857), Expect = 1e-96 Identities = 176/277 (63%), Positives = 208/277 (75%), Gaps = 5/277 (1%) Query: 1 MSDRYAVIGRPINHTKSPLIHGLFAQASNQQLEYGAIEGSL---DDFEAQVLQFRSEGGK 57 MSD+YAVIG PI HTKSPLIHGLF++ S+Q + Y AIEG L D F A V F + GGK Sbjct: 1 MSDQYAVIGNPIGHTKSPLIHGLFSEESHQDISYTAIEGPLEPDDAFAATVRSFFAAGGK 60 Query: 58 GMNITAPFKLRAFELADRRSERAQLARAANALKFEDGRIVAENFDGIGLLRDIEENLGEP 117 GMN+TAPFKL+AF +AD RSERA LA AAN L F DGRI+AENFDG+GL+RDIE NL P Sbjct: 61 GMNVTAPFKLKAFAMADERSERAALAGAANTLSFRDGRIIAENFDGVGLVRDIEVNLNLP 120 Query: 118 LRNRRVLLLGAGGAVRGALLPFLQAGPSELVIANRDMAK--ALALRNELDHSRLRISRYE 175 + +RVL+LGAGGAVRGALLPF+ A P+ELV+ANRD+AK AL R S + + Sbjct: 121 MAGKRVLVLGAGGAVRGALLPFIAARPAELVVANRDVAKVEALIARVATGDSLVACGYGD 180 Query: 176 ALEGQSFDIVVNATSASLTADLPPLPADVLGEAALAYELAYGKGLTPFLRLAREQGQARL 235 FD+VVNATSASL+ +LPP+P V AYEL YGK LTPFLR AR G + Sbjct: 181 LAAMGRFDLVVNATSASLSGELPPVPPSVFDPRGAAYELVYGKRLTPFLRHARHAGVLGI 240 Query: 236 ADGVGMLVEQAAEAFAWWRGVRPDTRAVINQLTIPLE 272 ADGVGMLVEQAAEAFAWWRG+RP+TRAVI++LT+PL+ Sbjct: 241 ADGVGMLVEQAAEAFAWWRGMRPETRAVIDRLTVPLD 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: 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 WP_011882038.1 (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.18782.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-74 235.8 0.0 3.1e-74 235.5 0.0 1.0 1 lcl|NCBI__GCF_000016205.1:WP_011882038.1 shikimate dehydrogenase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016205.1:WP_011882038.1 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 235.5 0.0 3.1e-74 3.1e-74 2 265 .. 4 272 .. 3 276 .. 0.95 Alignments for each domain: == domain 1 score: 235.5 bits; conditional E-value: 3.1e-74 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveiee...lekalsgikalglkGvnvTvPfKeev 67 ++viGnpi h ksplih + ++ ++++ Y+a+e ++e + ++ ++a+g kG+nvT PfK ++ lcl|NCBI__GCF_000016205.1:WP_011882038.1 4 QYAVIGNPIGHTKSPLIHGLFSEESHQDISYTAIEGPLEPddaFAATVRSFFAAGGKGMNVTAPFKLKA 72 69*******************************9876543336************************** PP TIGR00507 68 lellDeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavale 135 ++++De +e+a+l+ga NTl +dg+++++n Dg+Glv ++e l+ + ++krvl++GAGGa ++++l+ lcl|NCBI__GCF_000016205.1:WP_011882038.1 73 FAMADERSERAALAGAANTLSFRDGRIIAENFDGVGLVRDIEVnLNLPMAGKRVLVLGAGGAVRGALLP 141 ******************************************99************************* PP TIGR00507 136 Llka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkk.vdliinatsaglsgeideaevkae 202 + a + e+++aNR v+k e+l+ r+++ + +a ++ +dl++natsa+lsge+ ++v+++ lcl|NCBI__GCF_000016205.1:WP_011882038.1 142 FIAArPAELVVANRDVAKVEALIARVATGDSLVACGYGDLAAMGrFDLVVNATSASLSGEL--PPVPPS 208 *99889**********************99999999999988777****************..****** PP TIGR00507 203 llkegklvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdvekvfeal 265 +++ +++ lvy + tp+l+ a++ g ++dG+gMlv+Qaa +F w+g+ p+ v+++l lcl|NCBI__GCF_000016205.1:WP_011882038.1 209 VFDPRGAAYELVYGKRLTPFLRHARHAGvLGIADGVGMLVEQAAEAFAWWRGMRPETRAVIDRL 272 ****************************99*************************999988765 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.90 // [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