Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_011813853.1 HHAL_RS05380 shikimate dehydrogenase (NADP+)
Query= BRENDA::Q88RQ5 (274 letters) >NCBI__GCF_000015585.1:WP_011813853.1 Length = 270 Score = 267 bits (682), Expect = 2e-76 Identities = 146/269 (54%), Positives = 175/269 (65%), Gaps = 6/269 (2%) Query: 2 DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGG-NVT 60 D Y V GNPI HSKSP IH FA + G DL Y L AP D F+ A FF G G NVT Sbjct: 3 DHYAVVGNPIAHSKSPQIHTRFAAEVGADLHYHRLWAPEDHFAPVAEAFFAGGGHGLNVT 62 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120 VPFK A+ D+L+ RAR AGAVNTL DG GDNTDG GL+RDL N G++LAG+ Sbjct: 63 VPFKGAAYTFADTLSDRARAAGAVNTLRAEPDGRHFGDNTDGIGLLRDLQTNHGIDLAGR 122 Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQ-E 179 R+L+LGAGGA RGVL +L P+++VIANRTV++AE LA + A GF L E Sbjct: 123 RLLLLGAGGAARGVLHDLLGEDPRTVVIANRTVDRAEALAGNDHR---IRACGFDVLAGE 179 Query: 180 PVDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGL 239 +V+IN T+A L GE+PP+ D L+ G T YD++Y E TPF WA GA V DGL Sbjct: 180 RFEVVINTTAAGLQGEMPPLPDDLLAPGAT-AYDLVYADEDTPFMAWARARGAVTVCDGL 238 Query: 240 GMLAEQAAEAFFIWRGVRPDTAPVLAELR 268 GML EQAAE+F+ WRG P TAPV+ LR Sbjct: 239 GMLVEQAAESFYQWRGTYPQTAPVIEALR 267 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: 269 Number of extensions: 16 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: 274 Length of database: 270 Length adjustment: 25 Effective length of query: 249 Effective length of database: 245 Effective search space: 61005 Effective search space used: 61005 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_011813853.1 HHAL_RS05380 (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.6434.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-80 253.5 0.0 1.2e-79 253.3 0.0 1.0 1 lcl|NCBI__GCF_000015585.1:WP_011813853.1 HHAL_RS05380 shikimate dehydroge Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015585.1:WP_011813853.1 HHAL_RS05380 shikimate dehydrogenase (NADP+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 253.3 0.0 1.2e-79 1.2e-79 2 265 .. 4 266 .. 3 268 .. 0.95 Alignments for each domain: == domain 1 score: 253.3 bits; conditional E-value: 1.2e-79 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 ++v+Gnpi+hSksp ih +++++ g +l+Y+++ ++++++ + ++++a g +G+nvTvPfK +++ + lcl|NCBI__GCF_000015585.1:WP_011813853.1 4 HYAVVGNPIAHSKSPQIHTRFAAEVGADLHYHRLWAPEDHFAPVAEAFFAGGGHGLNVTVPFKGAAYTF 72 69******************************************************************* PP TIGR00507 71 lDeieesakligavNTlk.ledgklvgynTDgiGlvssLek..lsklksekrvliiGAGGaakavaleL 136 +D ++++a+++gavNTl+ dg+ g+nTDgiGl+ +L+ + l +++r+l++GAGGaa++v+ L lcl|NCBI__GCF_000015585.1:WP_011813853.1 73 ADTLSDRARAAGAVNTLRaEPDGRHFGDNTDGIGLLRDLQTnhGIDL-AGRRLLLLGAGGAARGVLHDL 140 ******************66699*****************9633344.59******************* PP TIGR00507 137 lka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaell 204 l + + +v+iaNRtv++ae+la ++ i a + + ++++++in+t+agl+ge+ ++++ +ll lcl|NCBI__GCF_000015585.1:WP_011813853.1 141 LGEdPRTVVIANRTVDRAEALAGNDHR---IRACGFDVLAGERFEVVINTTAAGLQGEM--PPLPDDLL 204 9886899***************99888...677777899********************..******** PP TIGR00507 205 kegklvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdvekvfeal 265 + g+ ++Dlvy+ +tp++++a+ +g v dGlgMlv+Qaa sF w+g+ p+ v+eal lcl|NCBI__GCF_000015585.1:WP_011813853.1 205 APGATAYDLVYADEDTPFMAWARARGaVTVCDGLGMLVEQAAESFYQWRGTYPQTAPVIEAL 266 **************************9999*************************9999986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (270 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: 10.04 // [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