Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate 209045 DVU0115 shikimate 5-dehydrogenase
Query= curated2:Q30VD9 (279 letters) >MicrobesOnline__882:209045 Length = 301 Score = 296 bits (759), Expect = 3e-85 Identities = 156/271 (57%), Positives = 185/271 (68%), Gaps = 2/271 (0%) Query: 5 RIPRQLYGIIGYPLGHSMSPLLHNWGFELLGEQAAYMAFPVAPEKLAEFICCARMLPVSG 64 RIP +LYGI+G+PLGH++SPLLHNWGF L A YMA+PV P + A F+ R LPV G Sbjct: 31 RIPERLYGIVGHPLGHTLSPLLHNWGFALHSLPAVYMAWPVPPGRFASFMEAVRTLPVHG 90 Query: 65 LSVTIPHKQAVMPLLDAVTPRAQAAGAVNTLFYDDGKLTGDNTDVYGFLHPLDSCGTAHA 124 SVTIPHK+ + L D VT RA+A GAVNTLF +DG + G+NTDV GFL PL + G Sbjct: 91 ASVTIPHKEEALRLCDRVTDRARAVGAVNTLFLEDGVVCGENTDVTGFLAPLRARGVRID 150 Query: 125 AALVLGAGGAANAVLAALTARGMCNVTVTNRNGDRARILAERFGVRCVAWEERHAVDADL 184 ALVLGAGGAA AVLA L G+ V ++NR D+A LA FG V W+ER + A L Sbjct: 151 EALVLGAGGAARAVLAGLVELGVRRVRISNRTHDKAMELAGAFGADVVPWDERGSAAAGL 210 Query: 185 VVNTTPLGMAGDRQAQTPLDPAFFSSRPAGLAYDLIYNPAQTFFLASAQAAGWRVLNGLD 244 VVNTTP GM G R ++PL FS R G+AYDL+YNP T FLA A+AAGW +GL Sbjct: 211 VVNTTPCGMQGARMGESPLPEGAFSGR--GMAYDLVYNPLTTRFLADARAAGWETQDGLG 268 Query: 245 MFVAQGAEQFRIWRGRELPFAQARALIADAL 275 MFV QG EQFRIW G +LP AR LIA+AL Sbjct: 269 MFVEQGREQFRIWTGLDLPAEGARRLIAEAL 299 Lambda K H 0.324 0.137 0.427 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: 247 Number of extensions: 9 Number of successful extensions: 2 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: 279 Length of database: 301 Length adjustment: 26 Effective length of query: 253 Effective length of database: 275 Effective search space: 69575 Effective search space used: 69575 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 48 (23.1 bits)
Align candidate 209045 DVU0115 (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.15906.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-71 225.5 0.0 3.9e-71 225.3 0.0 1.0 1 lcl|MicrobesOnline__882:209045 DVU0115 shikimate 5-dehydrogenas Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:209045 DVU0115 shikimate 5-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 225.3 0.0 3.9e-71 3.9e-71 2 269 .. 36 299 .. 35 300 .. 0.95 Alignments for each domain: == domain 1 score: 225.3 bits; conditional E-value: 3.9e-71 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeieesakl 80 l+g++G+p h +spl+hn ++ l +Y+a +v++ ++ ++++++++l+++G++vT+P+Kee+l+l+D+++++a++ lcl|MicrobesOnline__882:209045 36 LYGIVGHPLGHTLSPLLHNWGFALHSLPAVYMAWPVPPGRFASFMEAVRTLPVHGASVTIPHKEEALRLCDRVTDRARA 114 79***************************************************************************** PP TIGR00507 81 igavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka.dkeviiaNRtvekaeelae 158 +gavNTl ledg + g+nTD+ G+++ L+ ++ ++l++GAGGaa+av+ L++ +v i NRt +ka ela lcl|MicrobesOnline__882:209045 115 VGAVNTLFLEDGVVCGENTDVTGFLAPLRA-RGVR-IDEALVLGAGGAARAVLAGLVELgVRRVRISNRTHDKAMELAG 191 *****************************9.6666.679********************5578***************9 PP TIGR00507 159 rlqelgeilalsleevelkkvdliinatsaglsgeid.eaevkaellkegklvvDlvynpletpllkeakkkgtkvidG 236 ++ + ++ +e l++n+t+ g++g e +++++ ++ +++Dlvynpl t +l+ a+ g +++dG lcl|MicrobesOnline__882:209045 192 AFGA----DVVPWDERGSAAAGLVVNTTPCGMQGARMgESPLPEGAFSGRGMAYDLVYNPLTTRFLADARAAGWETQDG 266 9998....556666888889**************9988***************************************** PP TIGR00507 237 lgMlvaQaalsFelwtgvepdvekvfealkekl 269 lgM+v+Q+ +F++wtg + e +++ ++e+l lcl|MicrobesOnline__882:209045 267 LGMFVEQGREQFRIWTGLDLPAEGARRLIAEAL 299 ******************999999988888776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (301 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: 9.75 // [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