Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate BWI76_RS04655 BWI76_RS04655 shikimate dehydrogenase
Query= SwissProt::Q8Y9N5 (291 letters) >FitnessBrowser__Koxy:BWI76_RS04655 Length = 287 Score = 464 bits (1193), Expect = e-135 Identities = 228/287 (79%), Positives = 256/287 (89%) Query: 5 ITERITGHTELIGLIATPIRHSLSPTMHNEAFAKLGLDYVYLAFEVGDKELKDVVQGFRA 64 + ERITGHTELIGLIATPIRHS+SPTMHNEAFA LGLDYVYLAFEVG++ELKDVVQGFRA Sbjct: 1 MAERITGHTELIGLIATPIRHSMSPTMHNEAFAHLGLDYVYLAFEVGNEELKDVVQGFRA 60 Query: 65 MNLRGWNVSMPNKTNIHKYLDKLSPAAELVGAVNTVVNDDGVLTGHITDGTGYMRALKEA 124 + LRG NVSMPNKT I +YLDKLSPAAELVGAVNTVVND+GVLTGHITDGTGYMRALKE Sbjct: 61 LKLRGCNVSMPNKTEICQYLDKLSPAAELVGAVNTVVNDNGVLTGHITDGTGYMRALKEE 120 Query: 125 GHDIIGKKMTICGAGGAATAICIQAALDGVKEISIFNRKDDFYANAEKTVEKINSKTDCK 184 G DIIGKKMT+ GAGGAATA+C+QAALDGVK ISIFNRKD F+ANAE+TV KI + T C+ Sbjct: 121 GIDIIGKKMTVLGAGGAATALCVQAALDGVKAISIFNRKDKFFANAEQTVAKIRNNTRCE 180 Query: 185 AQLFDIEDHEQLRKEIAESVIFTNATGVGMKPFEGETLLPSADMLRPELIVSDVVYKPTK 244 LFD++DH++LR EI SVI TNATGVGMKPFEG+ LLP LRP+LIVSDVVY P K Sbjct: 181 IHLFDLDDHDKLRAEIDSSVILTNATGVGMKPFEGQMLLPDDSFLRPDLIVSDVVYNPRK 240 Query: 245 TRLLEIAEEQGCQTLNGLGMMLWQGAKAFEIWTHKEMPVDYIKEILF 291 T LLE+AE++GC+T+NGLGMMLWQGA+AFEIWT KEMPV++IK ILF Sbjct: 241 TYLLEVAEKKGCRTINGLGMMLWQGARAFEIWTGKEMPVEHIKSILF 287 Lambda K H 0.318 0.135 0.395 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: 347 Number of extensions: 5 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: 291 Length of database: 287 Length adjustment: 26 Effective length of query: 265 Effective length of database: 261 Effective search space: 69165 Effective search space used: 69165 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate BWI76_RS04655 BWI76_RS04655 (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.16055.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-70 221.3 0.0 7.6e-70 221.1 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS04655 BWI76_RS04655 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS04655 BWI76_RS04655 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 221.1 0.0 7.6e-70 7.6e-70 2 264 .. 11 285 .. 10 287 .] 0.89 Alignments for each domain: == domain 1 score: 221.1 bits; conditional E-value: 7.6e-70 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellD 72 l+g+i pi+hS+sp +hn+a+++lgl+++Ylafev eel+++++g++al l+G+nv +P K+e+ ++lD lcl|FitnessBrowser__Koxy:BWI76_RS04655 11 LIGLIATPIRHSMSPTMHNEAFAHLGLDYVYLAFEVGNEELKDVVQGFRALKLRGCNVSMPNKTEICQYLD 81 79********************************************************************* PP TIGR00507 73 eieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka.dk 141 ++++ a+l+gavNT++ ++g l g+ TDg G + +L++ + + +k++ ++GAGGaa a+ ++ + k lcl|FitnessBrowser__Koxy:BWI76_RS04655 82 KLSPAAELVGAVNTVVNDNGVLTGHITDGTGYMRALKEeGIDII-GKKMTVLGAGGAATALCVQAALDgVK 151 **************************************766677.8**************99987655378 PP TIGR00507 142 eviiaNRt...vekaeelaerlqe..lgeilalsleevelkk....vd.liinatsaglsgeideaevka. 201 +++i+NR ++ ae+ + ++++ ei ++l++ ++ + + ++ nat +g+++ ++ ++ lcl|FitnessBrowser__Koxy:BWI76_RS04655 152 AISIFNRKdkfFANAEQTVAKIRNntRCEIHLFDLDDHDKLRaeidSSvILTNATGVGMKPFEGQMLLPDd 222 9******833357888888888875344566778877776654533332456***********98888752 PP TIGR00507 202 ellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfea 264 + l+ + +v D+vynp +t ll+ a+kkg+++i+GlgM+ Q+a +Fe+wtg e +ve+++++ lcl|FitnessBrowser__Koxy:BWI76_RS04655 223 SFLRPDLIVSDVVYNPRKTYLLEVAEKKGCRTINGLGMMLWQGARAFEIWTGKEMPVEHIKSI 285 67899999*************************************************998875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (287 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: 9.17 // [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