Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_011883226.1 shikimate dehydrogenase
Query= BRENDA::Q88RQ5 (274 letters) >NCBI__GCF_000016205.1:WP_011883226.1 Length = 288 Score = 281 bits (719), Expect = 1e-80 Identities = 159/280 (56%), Positives = 185/280 (66%), Gaps = 9/280 (3%) Query: 2 DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGS-GGNVT 60 D+YVVFGNP+ HSKSP IH FA QTGQ L Y LAP+D F R F +G G NVT Sbjct: 11 DRYVVFGNPVAHSKSPFIHAQFAAQTGQALVYEHRLAPVDGFEAAVRAFVAEGGRGANVT 70 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120 VPFK +A L D+L+PRA AGAVNTL ADG + GDNTDG GLVRD+ N GV LAG Sbjct: 71 VPFKLDAHALADTLSPRAAAAGAVNTLRIEADGRIFGDNTDGVGLVRDIESNLGVSLAGA 130 Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREF----DELGPVVASGFAW 176 RIL+LGAGGA RGV+ P+L P S+ I NRT KAE L +F + G V++ G Sbjct: 131 RILLLGAGGAARGVVLPLLERAPLSITIVNRTASKAEALVGQFAQAAHDAGCVLSGGGPD 190 Query: 177 L--QEPVDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAK 234 + EP DVI+NAT+ SL L P D T+ YDMMYG +PT F Q A LG A+ Sbjct: 191 VVRAEPYDVIVNATAGSLDAAL-PACDPAAFGPHTLAYDMMYGAQPTVFMQHAASLG-AR 248 Query: 235 VLDGLGMLAEQAAEAFFIWRGVRPDTAPVLAELRRQLARG 274 DGLGML EQAAE+F+IWRGVRPD APVLA LR+ LA G Sbjct: 249 TADGLGMLVEQAAESFYIWRGVRPDGAPVLAALRQALAAG 288 Lambda K H 0.319 0.137 0.405 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: 271 Number of extensions: 15 Number of successful extensions: 5 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: 274 Length of database: 288 Length adjustment: 26 Effective length of query: 248 Effective length of database: 262 Effective search space: 64976 Effective search space used: 64976 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
Align candidate WP_011883226.1 (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.31414.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-81 257.3 0.0 7.7e-81 257.2 0.0 1.0 1 lcl|NCBI__GCF_000016205.1:WP_011883226.1 shikimate dehydrogenase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016205.1:WP_011883226.1 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.2 0.0 7.7e-81 7.7e-81 3 269 .. 13 285 .. 11 286 .. 0.95 Alignments for each domain: == domain 1 score: 257.2 bits; conditional E-value: 7.7e-81 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlell 71 + v+Gnp++hSksp+ih ++++q+g++l+Y + ++++ +e a+ ++ a+g +G+nvTvPfK + +l+ lcl|NCBI__GCF_000016205.1:WP_011883226.1 13 YVVFGNPVAHSKSPFIHAQFAAQTGQALVYEHRLAPVDGFEAAVRAFVAEGGRGANVTVPFKLDAHALA 81 78******************************************************************* PP TIGR00507 72 DeieesakligavNTlkle.dgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlk 138 D ++++a+++gavNTl++e dg++ g+nTDg+Glv ++e l ++ r+l++GAGGaa++v+l+Ll+ lcl|NCBI__GCF_000016205.1:WP_011883226.1 82 DTLSPRAAAAGAVNTLRIEaDGRIFGDNTDGVGLVRDIESnLGVSLAGARILLLGAGGAARGVVLPLLE 150 *****************76489******************9998888*******************987 PP TIGR00507 139 a.dkeviiaNRtvekaeelaerlqe....lgeilalsleevelkk.vdliinatsaglsgeideaevka 201 + +++i+NRt +kae+l+ ++++ g++l+ +v + +d+i+nat+ +l + ++ ++ lcl|NCBI__GCF_000016205.1:WP_011883226.1 151 RaPLSITIVNRTASKAEALVGQFAQaahdAGCVLSGGGPDVVRAEpYDVIVNATAGSLDAAL--PACDP 217 659******************9999887788888887777665555****************..9**** PP TIGR00507 202 ellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 + +l++D++y t++++ a ++g++++dGlgMlv+Qaa sF +w+gv pd v al+++l lcl|NCBI__GCF_000016205.1:WP_011883226.1 218 AAFGPHTLAYDMMYGAQPTVFMQHAASLGARTADGLGMLVEQAAESFYIWRGVRPDGAPVLAALRQAL 285 *********************************************************99999999887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (288 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: 11.17 // [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