Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate N515DRAFT_3118 N515DRAFT_3118 shikimate dehydrogenase (EC 1.1.1.25)
Query= BRENDA::Q88RQ5 (274 letters) >FitnessBrowser__Dyella79:N515DRAFT_3118 Length = 276 Score = 206 bits (525), Expect = 3e-58 Identities = 128/273 (46%), Positives = 150/273 (54%), Gaps = 8/273 (2%) Query: 3 QYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGS-GGNVTV 61 Q+ VFG+PI HS SP IH+ FA Q G LEY T+ A EF+ R FF G G NVT+ Sbjct: 5 QFAVFGHPIAHSLSPQIHQAFARQFGIALEYRTIDAAPAEFAASVRRFFAAGGRGANVTL 64 Query: 62 PFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGKR 121 P K AF L D + A R G N L+ L DG L NTDGAGLVRDLT ++L G Sbjct: 65 PHKAAAFELADERSEAAVRVGTANVLTPLPDGRLAAHNTDGAGLVRDLTERHRMDLRGHD 124 Query: 122 ILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQ--- 178 L+LGAGGA RGV +L ++L I NRT E A+ LA E P A W Sbjct: 125 ALLLGAGGAARGVAWSLLDAGVRTLTIVNRTPETADALADAIGE--PARAHTRYWEDLDD 182 Query: 179 -EPVDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLD 237 D+IINATSA + G+ + V R CYD+ YGK F WA A D Sbjct: 183 IGSFDLIINATSAGVLGKPLDLPFGFV-GNRATCYDLSYGKAAAGFVAWARAANALYAFD 241 Query: 238 GLGMLAEQAAEAFFIWRGVRPDTAPVLAELRRQ 270 GLGML E AA+AF +W G RPDT PV LRRQ Sbjct: 242 GLGMLVETAADAFELWHGKRPDTDPVHDALRRQ 274 Lambda K H 0.319 0.137 0.405 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: 245 Number of extensions: 9 Number of successful extensions: 4 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: 274 Length of database: 276 Length adjustment: 25 Effective length of query: 249 Effective length of database: 251 Effective search space: 62499 Effective search space used: 62499 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 N515DRAFT_3118 N515DRAFT_3118 (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.341.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-73 232.9 0.0 2.3e-73 232.6 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_3118 N515DRAFT_3118 shikimate dehydro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_3118 N515DRAFT_3118 shikimate dehydrogenase (EC 1.1.1.25) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 232.6 0.0 2.3e-73 2.3e-73 3 267 .. 6 273 .. 4 275 .. 0.94 Alignments for each domain: == domain 1 score: 232.6 bits; conditional E-value: 2.3e-73 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevl 68 ++v+G+pi+hS+sp ih+a+++q+g++leY +++ + e+ + ++a+g +G+nvT+P+K +++ lcl|FitnessBrowser__Dyella79:N515DRAFT_3118 6 FAVFGHPIAHSLSPQIHQAFARQFGIALEYRTIDAAPAEFAASVRRFFAAGGRGANVTLPHKAAAF 71 89**************************************************************** PP TIGR00507 69 ellDeieesakligavNTlk.ledgklvgynTDgiGlvssLek..lsklksekrvliiGAGGaaka 131 el+De +e a +g+ N l+ l dg+l ++nTDg Glv +L + l+ ++ +l++GAGGaa++ lcl|FitnessBrowser__Dyella79:N515DRAFT_3118 72 ELADERSEAAVRVGTANVLTpLPDGRLAAHNTDGAGLVRDLTErhRMDLR-GHDALLLGAGGAARG 136 *****************************************995445566.99************* PP TIGR00507 132 valeLlka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkk.vdliinatsaglsgeid 195 va +Ll+a +++i+NRt e a +la+++ e + e+++ +dliinatsag+ g+ lcl|FitnessBrowser__Dyella79:N515DRAFT_3118 137 VAWSLLDAgVRTLTIVNRTPETADALADAIGEPARAHTRYWEDLDDIGsFDLIINATSAGVLGKP- 201 ********55799*****************9966666666667766555**************99. PP TIGR00507 196 eaevkaellkegklvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdvek 260 ++ + + + + ++Dl y + + ++++a+ + dGlgMlv+ aa +Felw+g pd + lcl|FitnessBrowser__Dyella79:N515DRAFT_3118 202 -LDLPFGFVGNRATCYDLSYGKAAAGFVAWARAANaLYAFDGLGMLVETAADAFELWHGKRPDTDP 266 .999*******************************88999*************************9 PP TIGR00507 261 vfealke 267 v +al++ lcl|FitnessBrowser__Dyella79:N515DRAFT_3118 267 VHDALRR 273 9988875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (276 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: 10.47 // [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