Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_029911096.1 P166_RS0108345 shikimate dehydrogenase
Query= SwissProt::Q9KVT3 (278 letters) >NCBI__GCF_000711315.1:WP_029911096.1 Length = 281 Score = 258 bits (658), Expect = 1e-73 Identities = 138/278 (49%), Positives = 190/278 (68%), Gaps = 6/278 (2%) Query: 3 SQIDQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDG--FTEAAKHFFAQGGR 60 S +D YAV GNPI HSKSP IH LFA QT Q ++Y A + + F A + A+G + Sbjct: 2 SSVDCYAVVGNPIAHSKSPQIHRLFAEQTDQVLVYEAIRIDPEQTPFEYAVRQLMAKGYK 61 Query: 61 GCNVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDL-LAQQV 119 G NVTVPFK +AY+FA LTERA+ A AVNTLK +DG ILGDNTDG GLV D+ + Sbjct: 62 GLNVTVPFKLDAYQFATELTERAKTAQAVNTLKFGEDGSILGDNTDGIGLVNDIEINGNR 121 Query: 120 LLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFE 179 K +L++GAGGA +G+L+PLL++ PA++ + NRT KA++LAE + + A + Sbjct: 122 PFKDKRVLILGAGGAVQGILQPLLEKAPATVHIANRTAEKAQELAERFSNGIVMTASGWG 181 Query: 180 QL--KQSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQH-GCA 236 + +Q +D+IIN TSASL+ ++P I P S ++ YDMMYG TVF WA+QH Sbjct: 182 DIPCEQGFDIIINGTSASLENKVPLISPACLKSGNLVYDMMYGPKPTVFIDWAKQHQPSC 241 Query: 237 QAIDGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNL 274 Q +DGLGMLVGQAAE+F LWRG+RP T ++++++R+++ Sbjct: 242 QVMDGLGMLVGQAAEAFYLWRGVRPETARVIQQIRESI 279 Lambda K H 0.320 0.135 0.392 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: 202 Number of extensions: 8 Number of successful extensions: 5 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: 278 Length of database: 281 Length adjustment: 26 Effective length of query: 252 Effective length of database: 255 Effective search space: 64260 Effective search space used: 64260 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 WP_029911096.1 P166_RS0108345 (shikimate 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.23870.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-85 272.8 0.0 1.4e-85 272.7 0.0 1.0 1 lcl|NCBI__GCF_000711315.1:WP_029911096.1 P166_RS0108345 shikimate dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711315.1:WP_029911096.1 P166_RS0108345 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 272.7 0.0 1.4e-85 1.4e-85 2 269 .. 6 279 .. 5 280 .. 0.95 Alignments for each domain: == domain 1 score: 272.7 bits; conditional E-value: 1.4e-85 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveiee..lekalsgikalglkGvnvTvPfKeevl 68 +++v+Gnpi+hSksp ih +++q+++ l+Y a+ +++e+ +e+a+ ++ a+g kG+nvTvPfK ++ lcl|NCBI__GCF_000711315.1:WP_029911096.1 6 CYAVVGNPIAHSKSPQIHRLFAEQTDQVLVYEAIRIDPEQtpFEYAVRQLMAKGYKGLNVTVPFKLDAY 74 79***********************************99989*************************** PP TIGR00507 69 ellDeieesakligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavale 135 +++ e++e+ak+++avNTlk edg ++g+nTDgiGlv ++e +++ ++krvli+GAGGa ++++ + lcl|NCBI__GCF_000711315.1:WP_029911096.1 75 QFATELTERAKTAQAVNTLKfGEDGSILGDNTDGIGLVNDIEInGNRPFKDKRVLILGAGGAVQGILQP 143 ********************889******************987777777******************* PP TIGR00507 136 Llka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkk.vdliinatsaglsgeideaevkae 202 Ll++ + +v iaNRt eka+elaer+ + ++a +++ ++ +d+iin tsa+l++++ + +++ lcl|NCBI__GCF_000711315.1:WP_029911096.1 144 LLEKaPATVHIANRTAEKAQELAERFSNGIVMTASGWGDIPCEQgFDIIINGTSASLENKV--PLISPA 210 987669*********************955555556789**9999****************..****** PP TIGR00507 203 llkegklvvDlvynpletpllkeakkkg..tkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 lk+g+lv+D++y p+ t+++ +ak+++ ++v+dGlgMlv Qaa +F lw+gv p+ v+++++e + lcl|NCBI__GCF_000711315.1:WP_029911096.1 211 CLKSGNLVYDMMYGPKPTVFIDWAKQHQpsCQVMDGLGMLVGQAAEAFYLWRGVRPETARVIQQIRESI 279 **************************99889*********************************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (281 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.49 // [ok]
This GapMind analysis is from Apr 10 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