Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_013644226.1 METBO_RS03180 shikimate dehydrogenase
Query= SwissProt::Q58484 (282 letters) >NCBI__GCF_000191585.1:WP_013644226.1 Length = 286 Score = 300 bits (769), Expect = 2e-86 Identities = 156/286 (54%), Positives = 209/286 (73%), Gaps = 11/286 (3%) Query: 1 MINAKTKVIGLIGHPVEHSFSPIMHNAAFKDKGLNYVYVAFDVLPENLKYVIDGAKALGI 60 MI KT V G+IG PVEHS SP MHNAAFK+ G++ +YV F V E+L+ I GA++LG+ Sbjct: 1 MITGKTNVFGIIGDPVEHSLSPGMHNAAFKELGMDNIYVPFQVKAEHLEDAILGAQSLGV 60 Query: 61 VGFNVTIPHKIEIMKYLDEIDKDAQLIGAVNTIKIEDGKAIGYNTDGIGARMALEEEIGR 120 GFNVTIPHK E++ YLD +D A LIGAVNTI+ A+G+NTDGIGA MA+EE + Sbjct: 61 KGFNVTIPHKTEVINYLDYLDIAAGLIGAVNTIEFGKNGAVGHNTDGIGAVMAIEE-VTP 119 Query: 121 VKDKNIVIYGAGGAARAVAFELAKD--NNIIIANRTVEKAEALAKEIAEKLNKKFGEEVK 178 VK+K +VI GAGGA+RA+AF+L +N++IANRTVEKA L ++ EKL+ EV+ Sbjct: 120 VKNKKVVILGAGGASRAIAFQLLLSGVDNLVIANRTVEKAGELKTDLVEKLD----HEVR 175 Query: 179 FSGLDV----DLDGVDIIINATPIGMYPNIDVEPIVKAEKLREDMVVMDLIYNPLETVLL 234 SGLD +L I+IN TP+GMYPN+D +P+V AE + DMVV D++YNPL+T LL Sbjct: 176 VSGLDENLTQELSDTAILINTTPVGMYPNVDEKPVVTAEMMHPDMVVNDIVYNPLKTGLL 235 Query: 235 KEAKKVNAKTINGLGMLIYQGAVAFKIWTGVEPNIEVMKNAIIDKI 280 EA K AK+I+G+ ML+YQG AFKIWTG+EP +E+ + A+++++ Sbjct: 236 NEADKAGAKSISGIKMLMYQGVEAFKIWTGIEPPVEIFQRALMNEL 281 Lambda K H 0.318 0.139 0.385 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: 270 Number of extensions: 11 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: 282 Length of database: 286 Length adjustment: 26 Effective length of query: 256 Effective length of database: 260 Effective search space: 66560 Effective search space used: 66560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 bits)
Align candidate WP_013644226.1 METBO_RS03180 (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.16543.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-89 285.1 0.4 2.5e-89 285.0 0.4 1.0 1 lcl|NCBI__GCF_000191585.1:WP_013644226.1 METBO_RS03180 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000191585.1:WP_013644226.1 METBO_RS03180 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 285.0 0.4 2.5e-89 2.5e-89 2 269 .. 8 281 .. 7 282 .. 0.94 Alignments for each domain: == domain 1 score: 285.0 bits; conditional E-value: 2.5e-89 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 ++g+iG+p++hS+sp +hnaa+k+lg++ Y+ f+v+ e+le+a+ g+++lg+kG+nvT+P+K+ev+++ lcl|NCBI__GCF_000191585.1:WP_013644226.1 8 VFGIIGDPVEHSLSPGMHNAAFKELGMDNIYVPFQVKAEHLEDAILGAQSLGVKGFNVTIPHKTEVINY 76 79******************************************************************* PP TIGR00507 71 lDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka 139 lD ++ a ligavNT++ ++ +vg+nTDgiG+v+++e+++++k +k+v+i+GAGGa++a+a++Ll lcl|NCBI__GCF_000191585.1:WP_013644226.1 77 LDYLDIAAGLIGAVNTIEFGKNGAVGHNTDGIGAVMAIEEVTPVK-NKKVVILGAGGASRAIAFQLLLS 144 ********************99***********************.*******************9887 PP TIGR00507 140 .dkeviiaNRtvekaeel.aerlqelgeilalsleevelkk....vdliinatsaglsgeid.eaevka 201 +++iaNRtveka el ++ +++l +++ +s + +l + ++in+t++g+++++d ++ v+a lcl|NCBI__GCF_000191585.1:WP_013644226.1 145 gVDNLVIANRTVEKAGELkTDLVEKLDHEVRVSGLDENLTQelsdTAILINTTPVGMYPNVDeKPVVTA 213 4689***********99945667779999999988887766665578***************5667899 PP TIGR00507 202 ellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 e+++ +++v D+vynpl+t ll+ea k g+k i G+ Ml++Q++ +F++wtg+ep+ve +al ++l lcl|NCBI__GCF_000191585.1:WP_013644226.1 214 EMMHPDMVVNDIVYNPLKTGLLNEADKAGAKSISGIKMLMYQGVEAFKIWTGIEPPVEIFQRALMNEL 281 **********************************************************9998888776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (286 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: 8.38 // [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