Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate Pf1N1B4_1906 Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25)
Query= BRENDA::Q88RQ5 (274 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906 Length = 273 Score = 442 bits (1138), Expect = e-129 Identities = 216/272 (79%), Positives = 247/272 (90%) Query: 1 MDQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGGNVT 60 MD+YVVFGNPIGHSKSPLIHRLFAEQTGQ L+Y+TLLAPLD+FS CA+ FF++G G NVT Sbjct: 1 MDRYVVFGNPIGHSKSPLIHRLFAEQTGQKLDYSTLLAPLDDFSGCAQAFFREGRGANVT 60 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120 VPFKE+A+RL +SLT RA+RAGAVNTLSKLADG+L GDNTDGAGLVRDLTVNAG LAGK Sbjct: 61 VPFKEDAYRLANSLTKRAQRAGAVNTLSKLADGSLLGDNTDGAGLVRDLTVNAGFSLAGK 120 Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQEP 180 RIL+LGAGGAVRG LEP+LA +P S++IANRTVEKAE LA F +LGPV ASGF WLQEP Sbjct: 121 RILLLGAGGAVRGALEPLLAEQPASVIIANRTVEKAELLAELFADLGPVSASGFDWLQEP 180 Query: 181 VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGLG 240 VD+IINATSASL+G++PPIA SL+E G+TVCYDMMYGK+PT FC+WA++ GAA +DGLG Sbjct: 181 VDLIINATSASLSGDVPPIASSLIEPGKTVCYDMMYGKDPTSFCRWASEHGAAVAMDGLG 240 Query: 241 MLAEQAAEAFFIWRGVRPDTAPVLAELRRQLA 272 MLAEQAAEAF++WRGVRPDTAPVLAELRRQLA Sbjct: 241 MLAEQAAEAFYLWRGVRPDTAPVLAELRRQLA 272 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: 331 Number of extensions: 9 Number of successful extensions: 1 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: 273 Length adjustment: 25 Effective length of query: 249 Effective length of database: 248 Effective search space: 61752 Effective search space used: 61752 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 Pf1N1B4_1906 (Shikimate 5-dehydrogenase I alpha (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.9160.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-80 253.7 0.0 1e-79 253.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906 Shikimate 5-dehydrogenase I alph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906 Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 253.5 0.0 1e-79 1e-79 3 269 .. 4 271 .. 2 272 .. 0.94 Alignments for each domain: == domain 1 score: 253.5 bits; conditional E-value: 1e-79 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKee 66 + v+Gnpi hSksplih +++q+g++l Y + +++++++ ++++ +g +G+nvTvPfKe lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906 4 YVVFGNPIGHSKSPLIHRLFAEQTGQKLDYSTLLAPLDDFSGCAQAFFREG-RGANVTVPFKED 66 78***********************************************99.8*********** PP TIGR00507 67 vlellDeieesakligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGa 128 +++l+ ++++a+ +gavNTl l dg l+g+nTDg Glv +L + ++kr+l++GAGGa lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906 67 AYRLANSLTKRAQRAGAVNTLSkLADGSLLGDNTDGAGLVRDLTVnAGFSLAGKRILLLGAGGA 130 *********************99*********************98888888************ PP TIGR00507 129 akavaleLlka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsagls 191 ++++ +Ll + + +viiaNRtvekae lae ++ lg + a + ++ vdliinatsa+ls lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906 131 VRGALEPLLAEqPASVIIANRTVEKAELLAELFADLGPVSASGF-DWLQEPVDLIINATSASLS 193 ******98866489***********************9887665.455667************* PP TIGR00507 192 geideaevkaellkegk.lvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtg 253 g++ +++ ++l++ gk +++D++y + t + ++a+++g + +dGlgMl +Qaa +F lw+g lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906 194 GDV--PPIASSLIEPGKtVCYDMMYGKDPTSFCRWASEHGaAVAMDGLGMLAEQAAEAFYLWRG 255 ***..********98863789*******************66779******************* PP TIGR00507 254 vepdvekvfealkekl 269 v pd v l+++l lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906 256 VRPDTAPVLAELRRQL 271 *******999998887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (273 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.88 // [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