Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate NP_347533.1 CA_C0897 bifunctional chorismate mutase/shikimate 5-dehydrogenase
Query= curated2:A6M251 (270 letters) >NCBI__GCF_000008765.1:NP_347533.1 Length = 367 Score = 247 bits (630), Expect = 3e-70 Identities = 124/271 (45%), Positives = 184/271 (67%), Gaps = 9/271 (3%) Query: 4 YGLIGEKLSHSLSPKIHNTLFKDLKIEGAYKLFEVEKENLGKLIESIKLLKIKGVNVTIP 63 YGLIGEKL HS S IH +F+ + I+G Y LFEV KE L + +++ K++K G+NVTIP Sbjct: 101 YGLIGEKLGHSHSSYIHKLIFEKVGIKGIYNLFEVPKEKLKESVDTFKIIKCGGLNVTIP 160 Query: 64 YKQDVMEYLDFISDEAKKIGAVNTIYLEDNKLYGYNTDYYGFGTILNNNEIVIRDNVAMV 123 YK +VM+ L IS++A+KIGAVNT+ + G+NTDY GFG +L+ + I++N+ +V Sbjct: 161 YKVEVMKELYEISEKARKIGAVNTLKFSREGISGFNTDYIGFGKMLSKFRVEIKNNICVV 220 Query: 124 LGNGGAAKAVITYLLDHGIKKIYLVSRKIKGNSADKDERI--EFK--TYEEISEIKGDIL 179 LG+GGAA+AV+ YL D+ K IY+V+R + +K I EFK +Y+E+S +KGD++ Sbjct: 221 LGSGGAARAVLQYLKDNFAKDIYVVTR-----NPEKTSEIYGEFKVISYDELSNLKGDVI 275 Query: 180 INTTPLGMYPKVDDTPVNEDIINNFNSLIDIIYNPRETRFLKIGKNSNKKVCGGIEMLVG 239 IN TP GMYPK ++PV+++++ F+S +D+IYNP ET FLK + S K G+ MLV Sbjct: 276 INCTPKGMYPKEGESPVDKEVVAKFSSAVDLIYNPVETLFLKYARESGVKAVNGLYMLVS 335 Query: 240 QAIKAEEIWQECQLDNKLTQGLYSIFENEFK 270 QA +EEIW + +D + ++ + E + K Sbjct: 336 QAAASEEIWNDISIDEIIVDEIFEVLEEKIK 366 Lambda K H 0.316 0.139 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: 336 Number of extensions: 19 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: 270 Length of database: 367 Length adjustment: 27 Effective length of query: 243 Effective length of database: 340 Effective search space: 82620 Effective search space used: 82620 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: 48 (23.1 bits)
Align candidate NP_347533.1 CA_C0897 (bifunctional chorismate mutase/shikimate 5-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.15905.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-69 218.0 0.1 9.5e-69 217.5 0.1 1.2 1 lcl|NCBI__GCF_000008765.1:NP_347533.1 CA_C0897 bifunctional chorismate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008765.1:NP_347533.1 CA_C0897 bifunctional chorismate mutase/shikimate 5-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 217.5 0.1 9.5e-69 9.5e-69 2 266 .. 100 362 .. 99 366 .. 0.94 Alignments for each domain: == domain 1 score: 217.5 bits; conditional E-value: 9.5e-69 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDe 73 ++g+iG+ hS s ih+ ++++ g+++ Y fev+ e+l++ ++++k + G+nvT+P+K+ev++ l e lcl|NCBI__GCF_000008765.1:NP_347533.1 100 IYGLIGEKLGHSHSSYIHKLIFEKVGIKGIYNLFEVPKEKLKESVDTFKIIKCGGLNVTIPYKVEVMKELYE 171 79********************************************************************** PP TIGR00507 74 ieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka.dkev 143 i+e+a++igavNTlk + + g nTD iG+ + L+k ++k ++ +++G GGaa+av+ L+++ k++ lcl|NCBI__GCF_000008765.1:NP_347533.1 172 ISEKARKIGAVNTLKFSREGISGFNTDYIGFGKMLSKfRVEIK-NNICVVLGSGGAARAVLQYLKDNfAKDI 242 ***************9999******************667777.88999*****************999*** PP TIGR00507 144 iiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegklvvDlvy 215 ++ R ek+ e+ +ge + +s +e+ + k d+iin+t+ g++++ e +v++e++++ + +vDl+y lcl|NCBI__GCF_000008765.1:NP_347533.1 243 YVVTRNPEKTSEI------YGEFKVISYDELSNLKGDVIINCTPKGMYPKEGESPVDKEVVAKFSSAVDLIY 308 *********9554......788888*********************************************** PP TIGR00507 216 npletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepd...vekvfealk 266 np+et +lk+a++ g k ++Gl Mlv Qaa s e+w+ + +d v+++fe+l+ lcl|NCBI__GCF_000008765.1:NP_347533.1 309 NPVETLFLKYARESGVKAVNGLYMLVSQAAASEEIWNDISIDeiiVDEIFEVLE 362 ************************************999855222555555555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (367 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: 12.37 // [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