Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_029000830.1 H537_RS0130020 shikimate dehydrogenase
Query= BRENDA::Q88IJ7 (272 letters) >NCBI__GCF_000430725.1:WP_029000830.1 Length = 273 Score = 315 bits (806), Expect = 9e-91 Identities = 167/272 (61%), Positives = 199/272 (73%), Gaps = 1/272 (0%) Query: 1 MSDRYAVIGRPINHTKSPLIHGLFAQASNQQLEYGAIEGSLDDFEAQVLQFRSEGGKGMN 60 M+DRYA++G P+ +KSPLIH FA+ + Q +EY +E L F+ V FR+ G KG+N Sbjct: 1 MTDRYAIVGNPVGFSKSPLIHTEFARQTGQDIEYTRLEAPLGRFKETVDAFRAAGAKGVN 60 Query: 61 ITAPFKLRAFELADRRSERAQLARAANALKFEDGRIVAENFDGIGLLRDIEENLGEPLRN 120 ITAPFKL AF A SE A+LA AANAL FE R+ AENFDGIGL+ DI+ NLG L+ Sbjct: 61 ITAPFKLDAFAYASDVSEAARLAGAANALSFEGDRVRAENFDGIGLVNDIQRNLGFSLQG 120 Query: 121 RRVLLLGAGGAVRGALLPFLQAGPSELVIANRDMAKALALRNELDHS-RLRISRYEALEG 179 +RVL+LGAGGA RGALLPFL P+E V+ANR AKA AL + + + +R + LEG Sbjct: 121 KRVLMLGAGGAARGALLPFLAQQPAEFVLANRTAAKAQALARQCEGAGSIRGCGLQDLEG 180 Query: 180 QSFDIVVNATSASLTADLPPLPADVLGEAALAYELAYGKGLTPFLRLAREQGQARLADGV 239 FDIV+NATSASLT +LP +PA V G A LAYELAY KGLTPFLRLA+ G RLADGV Sbjct: 181 LRFDIVLNATSASLTGELPAVPASVFGSAQLAYELAYAKGLTPFLRLAQGAGVQRLADGV 240 Query: 240 GMLVEQAAEAFAWWRGVRPDTRAVINQLTIPL 271 GMLVEQAAEAF WWRGVRPDT +I QLT+PL Sbjct: 241 GMLVEQAAEAFQWWRGVRPDTAPLIRQLTVPL 272 Lambda K H 0.320 0.137 0.388 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: 225 Number of extensions: 9 Number of successful extensions: 2 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: 272 Length of database: 273 Length adjustment: 25 Effective length of query: 247 Effective length of database: 248 Effective search space: 61256 Effective search space used: 61256 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_029000830.1 H537_RS0130020 (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.3835.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-80 254.5 0.0 5.4e-80 254.4 0.0 1.0 1 lcl|NCBI__GCF_000430725.1:WP_029000830.1 H537_RS0130020 shikimate dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_029000830.1 H537_RS0130020 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 254.4 0.0 5.4e-80 5.4e-80 3 265 .. 5 268 .. 3 273 .] 0.97 Alignments for each domain: == domain 1 score: 254.4 bits; conditional E-value: 5.4e-80 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlell 71 ++++Gnp+ Sksplih ++++q+g+++eY+++e+++ ++++++++++a+g+kGvn+T PfK +++++ lcl|NCBI__GCF_000430725.1:WP_029000830.1 5 YAIVGNPVGFSKSPLIHTEFARQTGQDIEYTRLEAPLGRFKETVDAFRAAGAKGVNITAPFKLDAFAYA 73 9******************************************************************** PP TIGR00507 72 DeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka 139 +++e a+l+ga N l e++++ ++n DgiGlv ++++ l + ++krvl++GAGGaa++++l++l + lcl|NCBI__GCF_000430725.1:WP_029000830.1 74 SDVSEAARLAGAANALSFEGDRVRAENFDGIGLVNDIQRnLGFSLQGKRVLMLGAGGAARGALLPFLAQ 142 ****************************************999999******************98766 PP TIGR00507 140 .dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkeg 207 + e+++aNRt +ka++la +++ g+i l+++e ++d+++natsa+l+ge+ ++v+a+++ + lcl|NCBI__GCF_000430725.1:WP_029000830.1 143 qPAEFVLANRTAAKAQALARQCEGAGSIRGCGLQDLEGLRFDIVLNATSASLTGEL--PAVPASVFGSA 209 499*****************************************************..*********** PP TIGR00507 208 klvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdvekvfeal 265 +l++ l+y+++ tp+l++a+ g ++ +dG+gMlv+Qaa +F+ w+gv pd +++l lcl|NCBI__GCF_000430725.1:WP_029000830.1 210 QLAYELAYAKGLTPFLRLAQGAGvQRLADGVGMLVEQAAEAFQWWRGVRPDTAPLIRQL 268 ***********************999*************************99988876 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5.88 // [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