Align Shikimate dehydrogenase (NADP(+)); SD; SDH; EC 1.1.1.25 (characterized)
to candidate WP_012676742.1 PERMA_RS05330 shikimate dehydrogenase
Query= SwissProt::O67049 (269 letters) >NCBI__GCF_000021565.1:WP_012676742.1 Length = 281 Score = 275 bits (702), Expect = 1e-78 Identities = 135/278 (48%), Positives = 195/278 (70%), Gaps = 12/278 (4%) Query: 1 MINAQTQLYGVIGFPVKHSLSPVFQNALIRYAGLNAVYLAFEINPEELKKAFEGFKALKV 60 +IN +T++YG+ G+PVKHS SP+FQNA Y G+NAVYL F + PE+LK A EG +AL + Sbjct: 4 VINGETEVYGIFGYPVKHSKSPLFQNAAFSYLGINAVYLPFSVKPEDLKNAVEGIRALSI 63 Query: 61 KGINVTVPFKEEIIPLLDYVEDTAKEIGAVNTVKFENGKAYGYNTDWIGFLKSLKSLIPE 120 KG+N+TVP KEE++ L++ + + K IGA NT+K +G YNTD GF++ LK L+ Sbjct: 64 KGVNITVPHKEEVLKLVNEISEEVKYIGASNTIKNIDGYLIAYNTDAYGFIQGLKELVEN 123 Query: 121 VKEKSILVLGAGGASRAVIYALVKEGA-KVFLWNRTKEKAIKLAQKFP-----LEVVNSP 174 + K +LV+GAGGASRAV+Y L+KEGA K+++ NRT ++A + + F E + P Sbjct: 124 ISGKKVLVIGAGGASRAVVYGLIKEGAEKIYISNRTLKRAEDIIRDFSKLSRFTEKILEP 183 Query: 175 ------EEVIDKVQVIVNTTSVGLKDKDPEIFNYDLIKKDHVVVDIIYKETKLLKKAKEK 228 EE++ V +IVNTTSVGL+D+D +F+Y I+K H+VVDIIY++T LLK A+EK Sbjct: 184 LPLSQIEELLCNVDIIVNTTSVGLRDEDRPLFDYSKIEKRHIVVDIIYRKTPLLKAAEEK 243 Query: 229 GAKLFDGLPMLLWQGIEAFKIWNGCEVPYSVAERSVRD 266 G DGLPMLL+QG +F+IW G + P ++ ++++ D Sbjct: 244 GCLWQDGLPMLLYQGARSFEIWTGKKAPINIMKKALSD 281 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: 274 Number of extensions: 12 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: 269 Length of database: 281 Length adjustment: 25 Effective length of query: 244 Effective length of database: 256 Effective search space: 62464 Effective search space used: 62464 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_012676742.1 PERMA_RS05330 (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.3356.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-83 263.5 0.0 9.8e-83 263.4 0.0 1.0 1 lcl|NCBI__GCF_000021565.1:WP_012676742.1 PERMA_RS05330 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021565.1:WP_012676742.1 PERMA_RS05330 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 263.4 0.0 9.8e-83 9.8e-83 1 265 [. 10 279 .. 10 281 .] 0.92 Alignments for each domain: == domain 1 score: 263.4 bits; conditional E-value: 9.8e-83 TIGR00507 1 kllgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevle 69 +++g++G+p+khSkspl +naa++ lg++ +Yl f+v++e+l++a++gi+al +kGvn+TvP+Keevl+ lcl|NCBI__GCF_000021565.1:WP_012676742.1 10 EVYGIFGYPVKHSKSPLFQNAAFSYLGINAVYLPFSVKPEDLKNAVEGIRALSIKGVNITVPHKEEVLK 78 589****************************************************************** PP TIGR00507 70 llDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlk 138 l+ ei+e++k iga NT+k dg l++ynTD++G+++ L++l + s+k+vl+iGAGGa++av+ L k lcl|NCBI__GCF_000021565.1:WP_012676742.1 79 LVNEISEEVKYIGASNTIKNIDGYLIAYNTDAYGFIQGLKELVENISGKKVLVIGAGGASRAVVYGLIK 147 *****************************************777777********************** PP TIGR00507 139 a.dkeviiaNRtvekaeelaerlqe.....lgeilalsleevelkk..vdliinatsaglsgeideaev 199 + +++ i NRt+++ae+++ + + + l+l+++e+ vd+i+n+ts+gl+ e + lcl|NCBI__GCF_000021565.1:WP_012676742.1 148 EgAEKIYISNRTLKRAEDIIRDFSKlsrftEKILEPLPLSQIEELLcnVDIIVNTTSVGLRDED-RPLF 215 97789***************9999977753222233555555544344*************987.8999 PP TIGR00507 200 kaellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfeal 265 + +++++ ++vvD++y + tpllk a++kg+ +dGl Ml +Q+a sFe+wtg + +++ +++al lcl|NCBI__GCF_000021565.1:WP_012676742.1 216 DYSKIEKRHIVVDIIYRK--TPLLKAAEEKGCLWQDGLPMLLYQGARSFEIWTGKKAPINIMKKAL 279 ****************86..6***************************************999986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (281 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: 00:00:00.00 # Mc/sec: 8.39 // [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