Align Shikimate dehydrogenase (NADP(+)); SD; SDH; EC 1.1.1.25 (characterized)
to candidate WP_093393472.1 BM091_RS03440 shikimate dehydrogenase
Query= SwissProt::O67049 (269 letters) >NCBI__GCF_900114975.1:WP_093393472.1 Length = 278 Score = 179 bits (454), Expect = 6e-50 Identities = 106/265 (40%), Positives = 155/265 (58%), Gaps = 7/265 (2%) Query: 5 QTQLYGVIGFPVKHSLSPVFQNALIRYAGLNAVYLAFEINPEELKKAFEGFKALKVKGIN 64 QT+L+ VIG PVKHSLSP NA R + A YLA E++ + + + AL G++ Sbjct: 6 QTRLFAVIGHPVKHSLSPAMMNAAFRALDIPAFYLALEVS--DFLEDMKHITALGFDGLS 63 Query: 65 VTVPFKEEIIPLLDYVEDTAKEIGAVNTVKFENGKAYGYNTDWIGFLKSLKSLIPEVKEK 124 VT+P KE + L ++ A+ IGAVN +K + G NTDWIG + S KS ++ K Sbjct: 64 VTIPHKESAMKLAVVDDEAARAIGAVNCLKRVDDVWRGKNTDWIGVVDSFKSRGIDISGK 123 Query: 125 SILVLGAGGASRAVIYALVKEGAKVFLWNRTKEKAIKLAQKFPLEVV--NSPEEVIDKVQ 182 LVLGAGGA+R VIYA +K GA+V + NRT EKA LA +F + V S +E + Q Sbjct: 124 KALVLGAGGAARGVIYAALKMGAEVTVVNRTDEKAFSLADEFGINAVEHKSLKERVCDFQ 183 Query: 183 VIVNTTSVGLKDKDPEIF-NYDLIKKDHVVVDIIYK--ETKLLKKAKEKGAKLFDGLPML 239 V+ TT VG+ E F YD+ + +V+D++Y+ +T +K A+E+G + GL ML Sbjct: 184 VVFQTTPVGMNGYPVEHFWPYDIFRPGMIVMDLVYRPAKTAFMKSAEERGCTVISGLDML 243 Query: 240 LWQGIEAFKIWNGCEVPYSVAERSV 264 L+QG+ F+ W P ++++ Sbjct: 244 LYQGVAQFEWWFDRPAPLEAMKKAL 268 Lambda K H 0.318 0.138 0.396 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: 204 Number of extensions: 17 Number of successful extensions: 4 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: 269 Length of database: 278 Length adjustment: 25 Effective length of query: 244 Effective length of database: 253 Effective search space: 61732 Effective search space used: 61732 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: 47 (22.7 bits)
Align candidate WP_093393472.1 BM091_RS03440 (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.12269.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-70 223.1 0.0 2.3e-70 222.8 0.0 1.0 1 lcl|NCBI__GCF_900114975.1:WP_093393472.1 BM091_RS03440 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900114975.1:WP_093393472.1 BM091_RS03440 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 222.8 0.0 2.3e-70 2.3e-70 2 267 .. 9 270 .. 8 272 .. 0.93 Alignments for each domain: == domain 1 score: 222.8 bits; conditional E-value: 2.3e-70 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 l++viG+p+khS+sp++ naa++ l++ Yla+ev ++ + ++ i alg+ G++vT+P+Ke++++l lcl|NCBI__GCF_900114975.1:WP_093393472.1 9 LFAVIGHPVKHSLSPAMMNAAFRALDIPAFYLALEV--SDFLEDMKHITALGFDGLSVTIPHKESAMKL 75 79******************************9887..57888899*********************** PP TIGR00507 71 lDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka 139 + +e a++igavN lk+ d+ g+nTD iG+v s + s+k++l++GAGGaa++v+ + lk+ lcl|NCBI__GCF_900114975.1:WP_093393472.1 76 AVVDDEAARAIGAVNCLKRVDDVWRGKNTDWIGVVDSFKSRGIDISGKKALVLGAGGAARGVIYAALKM 144 *999999********************************9555556*********************** PP TIGR00507 140 dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegk 208 + ev+++NRt eka la+++ + + + + + + ++ ++t++g++g e + ++++ g+ lcl|NCBI__GCF_900114975.1:WP_093393472.1 145 GAEVTVVNRTDEKAFSLADEFGI--NAVEHKSLKERVCDFQVVFQTTPVGMNGYPVEHFWPYDIFRPGM 211 ********************998..44444445566667**************999************* PP TIGR00507 209 lvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealke 267 +v+Dlvy p +t+++k a+++g+ vi Gl+Ml +Q++ +Fe w+ ++e +++al e lcl|NCBI__GCF_900114975.1:WP_093393472.1 212 IVMDLVYRPAKTAFMKSAEERGCTVISGLDMLLYQGVAQFEWWFDRPAPLEAMKKALYE 270 *****************************************************998865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (278 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: 6.35 // [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