Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate 6935834 Sama_0052 shikimate dehydrogenase (RefSeq)
Query= BRENDA::Q88RQ5 (274 letters) >FitnessBrowser__SB2B:6935834 Length = 278 Score = 288 bits (737), Expect = 9e-83 Identities = 156/274 (56%), Positives = 193/274 (70%), Gaps = 5/274 (1%) Query: 2 DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGS-GGNVT 60 D++ VFGNPI HSKSP IH +FA++TGQ L Y +LAPLD F++ F G G NVT Sbjct: 8 DRFAVFGNPISHSKSPQIHAMFAKETGQTLTYEAILAPLDGFAEAVTAFMAAGGCGANVT 67 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120 VPFKE+AF LCD L+ AR AGAVNTL KL DG L+GDNTDG GLV DL + GVEL K Sbjct: 68 VPFKEQAFTLCDELSDDARIAGAVNTLIKLPDGRLRGDNTDGMGLVADL-IRHGVELNNK 126 Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQEP 180 R+L++GAGGA RG L P L L I+NRT+ KAE LA ++ V SG + ++ P Sbjct: 127 RVLLVGAGGAARGALLP-LVRAGAKLTISNRTLSKAEALAALCPKVNVEVISG-SHIRSP 184 Query: 181 VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGLG 240 DVIIN+TSASL+G+LP IA + ++ +TVCYDMMYG +PT F +WA LGA +DGLG Sbjct: 185 FDVIINSTSASLSGDLPVIAANAID-NQTVCYDMMYGAKPTVFNEWARSLGAKICIDGLG 243 Query: 241 MLAEQAAEAFFIWRGVRPDTAPVLAELRRQLARG 274 ML QAAE+F++WR VRP+ APVL LR+ L G Sbjct: 244 MLVGQAAESFYLWRRVRPNAAPVLQTLRQSLISG 277 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: 244 Number of extensions: 13 Number of successful extensions: 6 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: 278 Length adjustment: 25 Effective length of query: 249 Effective length of database: 253 Effective search space: 62997 Effective search space used: 62997 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 6935834 Sama_0052 (shikimate 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.20857.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-86 276.1 0.0 1.4e-86 275.9 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6935834 Sama_0052 shikimate dehydrogenas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6935834 Sama_0052 shikimate dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 275.9 0.0 1.4e-86 1.4e-86 3 269 .. 10 274 .. 8 275 .. 0.95 Alignments for each domain: == domain 1 score: 275.9 bits; conditional E-value: 1.4e-86 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeieesak 79 ++v+Gnpi hSksp ih ++k++g++l+Y a+ ++++ + +a++++ a+g G+nvTvPfKe+++ l+De++++a+ lcl|FitnessBrowser__SB2B:6935834 10 FAVFGNPISHSKSPQIHAMFAKETGQTLTYEAILAPLDGFAEAVTAFMAAGGCGANVTVPFKEQAFTLCDELSDDAR 86 89*************************************************************************** PP TIGR00507 80 ligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlkadkeviiaNRtvekae 154 +gavNTl l dg+l g+nTDg+Glv++L + +l+ +krvl++GAGGaa++++l+L++a+ +++i NRt++kae lcl|FitnessBrowser__SB2B:6935834 87 IAGAVNTLIkLPDGRLRGDNTDGMGLVADLIRhGVELN-NKRVLLVGAGGAARGALLPLVRAGAKLTISNRTLSKAE 162 *******977**********************556666.************************************** PP TIGR00507 155 elaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegklvvDlvynpletpllkeakkkgt 231 +la +++ ++ +s ++++ + +d+iin+tsa+lsg++ + + a+ ++++++++D++y + t++ ++a+++g+ lcl|FitnessBrowser__SB2B:6935834 163 ALAALCPK-VNVEVISGSHIR-SPFDVIINSTSASLSGDL--PVIAANAIDNQTVCYDMMYGAKPTVFNEWARSLGA 235 *******9.667778877776.46****************..9*********************************6 PP TIGR00507 232 k.vidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 k idGlgMlv Qaa sF lw+ v p+ v ++l++ l lcl|FitnessBrowser__SB2B:6935834 236 KiCIDGLGMLVGQAAESFYLWRRVRPNAAPVLQTLRQSL 274 6169*************************9999988776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (278 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.90 // [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