Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate 8501228 DvMF_1962 shikimate 5-dehydrogenase (RefSeq)
Query= curated2:Q30VD9 (279 letters) >FitnessBrowser__Miya:8501228 Length = 315 Score = 290 bits (743), Expect = 2e-83 Identities = 158/292 (54%), Positives = 191/292 (65%), Gaps = 17/292 (5%) Query: 4 PRIPRQLYGIIGYPLGHSMSPLLHNWGFELLGEQAAYMAFPVAPEKLAEFICCARMLPVS 63 P +PR+LYGIIG+PLGH+MSPLLHNWGF LL A YMA+P+ P ++ +FI R LP+ Sbjct: 5 PFLPRELYGIIGHPLGHTMSPLLHNWGFSLLDVPAVYMAWPLEPGRVGDFITAVRTLPIR 64 Query: 64 GLSVTIPHKQAVMPLLDAVTPRAQAAGAVNTLFYDDGKLTGDNTDVYGFLHPL---DSCG 120 G SVTIPHKQAV+PLLD V+ RA+A GAVNTL++ DG+L G+NTDV GFL PL + G Sbjct: 65 GASVTIPHKQAVLPLLDGVSDRARAVGAVNTLYWRDGQLLGENTDVTGFLAPLRQRAAAG 124 Query: 121 TAHAAALVLGAGGAANAVLAALTARGMCN------VTVTNRNGDRARILAERFGVRCVAW 174 ALVLG GGAA AVLA L G V VT RN ++A LA FG V W Sbjct: 125 WRCERALVLGNGGAARAVLAGLRELGPAGDGVVRAVGVTGRNAEKAAPLAAEFGAEVVDW 184 Query: 175 EERHAVDADLVVNTTPLGMAGDRQAQTPLDPAFFSSRPA--------GLAYDLIYNPAQT 226 + R ADLVVNTTP+GM+G+RQ T F+++ GLAYDL+YNP +T Sbjct: 185 DARVHWGADLVVNTTPMGMSGERQGDTAFPEQGFAAQGVAAGGDGRRGLAYDLVYNPLRT 244 Query: 227 FFLASAQAAGWRVLNGLDMFVAQGAEQFRIWRGRELPFAQARALIADALASG 278 FL+ A AGW +GL MFV QG EQFR+W G ELP AR L+A AL G Sbjct: 245 RFLSEAADAGWDTQDGLGMFVEQGREQFRLWTGLELPAEGARTLVAVALGLG 296 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: 304 Number of extensions: 13 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: 279 Length of database: 315 Length adjustment: 26 Effective length of query: 253 Effective length of database: 289 Effective search space: 73117 Effective search space used: 73117 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 8501228 DvMF_1962 (shikimate 5-dehydrogenase (RefSeq))
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.27768.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-64 201.1 0.0 1.3e-63 200.6 0.0 1.2 1 lcl|FitnessBrowser__Miya:8501228 DvMF_1962 shikimate 5-dehydrogen Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501228 DvMF_1962 shikimate 5-dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 200.6 0.0 1.3e-63 1.3e-63 2 266 .. 11 290 .. 10 294 .. 0.86 Alignments for each domain: == domain 1 score: 200.6 bits; conditional E-value: 1.3e-63 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeieesa 78 l+g+iG+p h +spl+hn ++ l++ +Y+a ++e+ ++ ++++++++l+++G++vT+P+K++vl+llD ++++a lcl|FitnessBrowser__Miya:8501228 11 LYGIIGHPLGHTMSPLLHNWGFSLLDVPAVYMAWPLEPGRVGDFITAVRTLPIRGASVTIPHKQAVLPLLDGVSDRA 87 89*************************************************************************** PP TIGR00507 79 kligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlkad.......keviiaN 147 +++gavNTl +dg+l+g+nTD+ G+++ L++ +r+l++G GGaa+av+ L + + +v ++ lcl|FitnessBrowser__Miya:8501228 88 RAVGAVNTLYWRDGQLLGENTDVTGFLAPLRQrAAAGWRCERALVLGNGGAARAVLAGLRELGpagdgvvRAVGVTG 164 ********************************655545589****************99987522233334677889 PP TIGR00507 148 Rtvekaeelaerlqelgeilalsleevelkk.vdliinatsaglsgeid.eaevkaellkegk..........lvvD 212 R eka la ++ + e++ ++ + + dl++n+t++g+sge + +++ +++ ++++ l++D lcl|FitnessBrowser__Miya:8501228 165 RNAEKAAPLAAEFGA--EVVDWD---ARVHWgADLVVNTTPMGMSGERQgDTAFPEQGFAAQGvaaggdgrrgLAYD 236 998888888888877..666676...3334349**************9999999888776543111122222378** PP TIGR00507 213 lvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealk 266 lvynpl t +l+ea + g ++dGlgM+v+Q+ +F+lwtg e + e ++ ++ lcl|FitnessBrowser__Miya:8501228 237 LVYNPLRTRFLSEAADAGWDTQDGLGMFVEQGREQFRLWTGLELPAEGARTLVA 290 ******************************************998888776665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (315 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: 12.06 // [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