Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate WP_012475169.1 CPHAMN1_RS08845 shikimate dehydrogenase (NADP+)
Query= curated2:B3ELA4 (293 letters) >NCBI__GCF_000020545.1:WP_012475169.1 Length = 293 Score = 581 bits (1498), Expect = e-171 Identities = 293/293 (100%), Positives = 293/293 (100%) Query: 1 MYSAKKILGLIGRNVGYSYSPYIHNTAAEKLGLGYYYTIFNISSHDLVPSALEGAKALGI 60 MYSAKKILGLIGRNVGYSYSPYIHNTAAEKLGLGYYYTIFNISSHDLVPSALEGAKALGI Sbjct: 1 MYSAKKILGLIGRNVGYSYSPYIHNTAAEKLGLGYYYTIFNISSHDLVPSALEGAKALGI 60 Query: 61 AGFNVTIPYKKTVVACMDKLSPEAEAIGAVNTIVNDNGTLIGYNTDIAGIVIPLEPYASM 120 AGFNVTIPYKKTVVACMDKLSPEAEAIGAVNTIVNDNGTLIGYNTDIAGIVIPLEPYASM Sbjct: 61 AGFNVTIPYKKTVVACMDKLSPEAEAIGAVNTIVNDNGTLIGYNTDIAGIVIPLEPYASM 120 Query: 121 IDAQPVGIFGNGGAAMAAIEALSTCFTPSGIRLFVRQREKGSELCRQFKDKNLPIPLSTH 180 IDAQPVGIFGNGGAAMAAIEALSTCFTPSGIRLFVRQREKGSELCRQFKDKNLPIPLSTH Sbjct: 121 IDAQPVGIFGNGGAAMAAIEALSTCFTPSGIRLFVRQREKGSELCRQFKDKNLPIPLSTH 180 Query: 181 TLDDHTAQHNCRLLINATPIGTKGLDTAPAGSIIPSGSGVVHSGQIIFDMVYNPVETQLL 240 TLDDHTAQHNCRLLINATPIGTKGLDTAPAGSIIPSGSGVVHSGQIIFDMVYNPVETQLL Sbjct: 181 TLDDHTAQHNCRLLINATPIGTKGLDTAPAGSIIPSGSGVVHSGQIIFDMVYNPVETQLL 240 Query: 241 QLAKATGAIAIPGIEMLIGQASRSFEIWTGKAMPVTTVRNKLQELLLTEKRSS 293 QLAKATGAIAIPGIEMLIGQASRSFEIWTGKAMPVTTVRNKLQELLLTEKRSS Sbjct: 241 QLAKATGAIAIPGIEMLIGQASRSFEIWTGKAMPVTTVRNKLQELLLTEKRSS 293 Lambda K H 0.318 0.135 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: 495 Number of extensions: 11 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: 293 Length of database: 293 Length adjustment: 26 Effective length of query: 267 Effective length of database: 267 Effective search space: 71289 Effective search space used: 71289 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 WP_012475169.1 CPHAMN1_RS08845 (shikimate dehydrogenase (NADP+))
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.22125.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-65 206.9 0.0 1.9e-65 206.7 0.0 1.0 1 lcl|NCBI__GCF_000020545.1:WP_012475169.1 CPHAMN1_RS08845 shikimate dehydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020545.1:WP_012475169.1 CPHAMN1_RS08845 shikimate dehydrogenase (NADP+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 206.7 0.0 1.9e-65 1.9e-65 1 269 [. 6 286 .. 6 287 .. 0.91 Alignments for each domain: == domain 1 score: 206.7 bits; conditional E-value: 1.9e-65 TIGR00507 1 kllgviGnpikhSksplihnaalkqlgleleYlafeveiee.lekalsgikalglkGvnvTvPfKeevl 68 k+lg+iG + S sp ihn a+++lgl + Y+ f+++ ++ +++al+g+kalg+ G+nvT+P+K+ v+ lcl|NCBI__GCF_000020545.1:WP_012475169.1 6 KILGLIGRNVGYSYSPYIHNTAAEKLGLGYYYTIFNISSHDlVPSALEGAKALGIAGFNVTIPYKKTVV 74 689*********************************998885799************************ PP TIGR00507 69 ellDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLl 137 + +D+++++a++igavNT++ ++g l+gynTD G+v Le + + + v i G GGaa a++ +L+ lcl|NCBI__GCF_000020545.1:WP_012475169.1 75 ACMDKLSPEAEAIGAVNTIVNDNGTLIGYNTDIAGIVIPLEPYASMIDAQPVGIFGNGGAAMAAIEALS 143 ******************************************888888********************9 PP TIGR00507 138 ka..dkeviiaNRtvekaeelaerlqelgeilalsleevelkk....vdliinatsaglsgeid...ea 197 ++ + ++ R ek+ el +++ + ls++ ++ ++ l+inat++g +g lcl|NCBI__GCF_000020545.1:WP_012475169.1 144 TCftPSGIRLFVRQREKGSELCRQFKDKNLPIPLSTHTLDDHTaqhnCRLLINATPIGTKGLDTapaGS 212 977799*********************8888888887777665444589********998743313345 PP TIGR00507 198 evk..aellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfea 264 +++ ++++++g++++D+vynp+et ll++ak g+ i G++Ml+ Qa sFe+wtg +v v+++ lcl|NCBI__GCF_000020545.1:WP_012475169.1 213 IIPsgSGVVHSGQIIFDMVYNPVETQLLQLAKATGAIAIPGIEMLIGQASRSFEIWTGKAMPVTTVRNK 281 565225689***********************************************************9 PP TIGR00507 265 lkekl 269 l+e l lcl|NCBI__GCF_000020545.1:WP_012475169.1 282 LQELL 286 99865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (293 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: 8.81 // [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