Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_069665194.1 BCR25_RS19030 shikimate dehydrogenase
Query= SwissProt::Q8Y9N5 (291 letters) >NCBI__GCF_001730305.1:WP_069665194.1 Length = 289 Score = 280 bits (715), Expect = 4e-80 Identities = 137/283 (48%), Positives = 190/283 (67%) Query: 8 RITGHTELIGLIATPIRHSLSPTMHNEAFAKLGLDYVYLAFEVGDKELKDVVQGFRAMNL 67 +ITG+T L L ATPIRHS+SP +HN AF LG+D VYLAFEVG L+ + R +++ Sbjct: 4 KITGNTRLAALFATPIRHSVSPIIHNTAFQALGIDAVYLAFEVGPDGLEQAIASIRNLDM 63 Query: 68 RGWNVSMPNKTNIHKYLDKLSPAAELVGAVNTVVNDDGVLTGHITDGTGYMRALKEAGHD 127 G N+SMPNK ++DKLS AA L+GA+NT+ N DG L GH TDG G+MR+L + Sbjct: 64 LGANLSMPNKLLAVNHMDKLSEAARLIGAINTITNQDGFLVGHNTDGIGFMRSLHDMNVT 123 Query: 128 IIGKKMTICGAGGAATAICIQAALDGVKEISIFNRKDDFYANAEKTVEKINSKTDCKAQL 187 IIG KMT+ GAGGAA AI QAALDGVKEI+++NR Y A+ + I +T+C+ L Sbjct: 124 IIGHKMTVLGAGGAAAAIIAQAALDGVKEIAVYNRNSRSYEQAKAKLRYIAEQTNCRITL 183 Query: 188 FDIEDHEQLRKEIAESVIFTNATGVGMKPFEGETLLPSADMLRPELIVSDVVYKPTKTRL 247 D+ D + L +++ ES + N T VGMKP E T + ++ P+L+V D +Y P +T Sbjct: 184 NDLADEKALAQDVGESRLLLNTTSVGMKPLEKATPIQDFSIIGPDLVVYDAIYTPRETAF 243 Query: 248 LEIAEEQGCQTLNGLGMMLWQGAKAFEIWTHKEMPVDYIKEIL 290 L+ A +G T NGLGM+L+QGA+AF++WT +E+P+ +K I+ Sbjct: 244 LKQARLRGALTANGLGMLLYQGAEAFKLWTGQELPISIVKPII 286 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: 264 Number of extensions: 13 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: 289 Length adjustment: 26 Effective length of query: 265 Effective length of database: 263 Effective search space: 69695 Effective search space used: 69695 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_069665194.1 BCR25_RS19030 (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.1272937.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-68 215.6 0.1 4.2e-68 215.4 0.1 1.0 1 NCBI__GCF_001730305.1:WP_069665194.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001730305.1:WP_069665194.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 215.4 0.1 4.2e-68 4.2e-68 2 265 .. 11 286 .. 10 289 .] 0.85 Alignments for each domain: == domain 1 score: 215.4 bits; conditional E-value: 4.2e-68 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDei 74 l +++ pi+hS+sp+ihn a++ lg++ +Ylafev ++ le+a+ i++l + G+n+ +P K +++ +D++ NCBI__GCF_001730305.1:WP_069665194.1 11 LAALFATPIRHSVSPIIHNTAFQALGIDAVYLAFEVGPDGLEQAIASIRNLDMLGANLSMPNKLLAVNHMDKL 83 5799********************************************************************* PP TIGR00507 75 eesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka.dkeviia 146 +e a+liga+NT++ +dg lvg+nTDgiG++ sL+ ++ ++++ ++GAGGaa a++ + + ke+ + NCBI__GCF_001730305.1:WP_069665194.1 84 SEAARLIGAINTITNQDGFLVGHNTDGIGFMRSLHDMNVTIIGHKMTVLGAGGAAAAIIAQAALDgVKEIAVY 156 ************************************888888***************987765443899**** PP TIGR00507 147 NR...tvekaeelaerlqe.lgeilalsleevelkk........vdliinatsaglsgeid.eaevkaellke 206 NR + e+a++ + ++e + + + l+++ +k l++n+ts+g+++ + ++ + +++ NCBI__GCF_001730305.1:WP_069665194.1 157 NRnsrSYEQAKAKLRYIAEqT--NCRITLNDLADEKalaqdvgeSRLLLNTTSVGMKPLEKaTPIQDFSIIGP 227 *82224567777666676632..333333333333223223233569**********9877355556799999 PP TIGR00507 207 gklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfeal 265 + +v+D +y p et++lk a+ +g+ +++GlgMl +Q+a +F+lwtg+e +++ v+ ++ NCBI__GCF_001730305.1:WP_069665194.1 228 DLVVYDAIYTPRETAFLKQARLRGALTANGLGMLLYQGAEAFKLWTGQELPISIVKPII 286 *************************************************9998887655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (289 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 15.25 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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