Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_029134830.1 A3GO_RS0119540 shikimate dehydrogenase
Query= BRENDA::Q88RQ5 (274 letters) >NCBI__GCF_000428045.1:WP_029134830.1 Length = 270 Score = 296 bits (757), Expect = 4e-85 Identities = 159/269 (59%), Positives = 187/269 (69%), Gaps = 3/269 (1%) Query: 2 DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGG-NVT 60 D+Y V GNPI HSKSPLIHR FAEQTG DL Y LL LD F R FF G G NVT Sbjct: 3 DRYAVIGNPIEHSKSPLIHRAFAEQTGMDLTYERLLGRLDGFDKDVRKFFAGGGRGLNVT 62 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120 VPFKE+A+ L D TPRA AGAVNTL L G L+GDNTDGAGLVRDL+VN G L+G Sbjct: 63 VPFKEQAWALADERTPRAGSAGAVNTLVPLDAGRLRGDNTDGAGLVRDLSVNHGYLLSGC 122 Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQ-E 179 RIL+LGAGGA +GV+ P+L P+ LVIANRT +KA +LA LGP+ G L+ + Sbjct: 123 RILLLGAGGASKGVVRPLLECGPEQLVIANRTADKARRLAATLQPLGPIRGCGLDELEGD 182 Query: 180 PVDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGL 239 D+IIN T+A L GE+PP+ ++ AG YDM+Y EPT F +W + A K LDGL Sbjct: 183 RFDLIINGTAAGLQGEVPPLPSGILTAGGWT-YDMVYASEPTAFVRWGQRHRAGKALDGL 241 Query: 240 GMLAEQAAEAFFIWRGVRPDTAPVLAELR 268 GML EQAAE+F +WRGVRPDTAPV+A LR Sbjct: 242 GMLVEQAAESFLLWRGVRPDTAPVIASLR 270 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: 285 Number of extensions: 14 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_029134830.1 A3GO_RS0119540 (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.18752.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-84 268.0 0.0 4.1e-84 267.9 0.0 1.0 1 lcl|NCBI__GCF_000428045.1:WP_029134830.1 A3GO_RS0119540 shikimate dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000428045.1:WP_029134830.1 A3GO_RS0119540 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 267.9 0.0 4.1e-84 4.1e-84 3 263 .. 5 267 .. 3 270 .] 0.98 Alignments for each domain: == domain 1 score: 267.9 bits; conditional E-value: 4.1e-84 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlell 71 ++viGnpi+hSksplih a+++q+g++l+Y ++ +++ + k + +++a g +G+nvTvPfKe++ +l+ lcl|NCBI__GCF_000428045.1:WP_029134830.1 5 YAVIGNPIEHSKSPLIHRAFAEQTGMDLTYERLLGRLDGFDKDVRKFFAGGGRGLNVTVPFKEQAWALA 73 9******************************************************************** PP TIGR00507 72 DeieesakligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlk 138 De +++a +gavNTl+ l+ g+l g+nTDg Glv +L+ l s+ r+l++GAGGa+k+v+ +Ll+ lcl|NCBI__GCF_000428045.1:WP_029134830.1 74 DERTPRAGSAGAVNTLVpLDAGRLRGDNTDGAGLVRDLSVnHGYLLSGCRILLLGAGGASKGVVRPLLE 142 ***************************************98999************************* PP TIGR00507 139 a.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellke 206 +++++iaNRt +ka++la +lq lg i l+e+e +++dliin t+agl+ge+ +++++++l++ lcl|NCBI__GCF_000428045.1:WP_029134830.1 143 CgPEQLVIANRTADKARRLAATLQPLGPIRGCGLDELEGDRFDLIINGTAAGLQGEV--PPLPSGILTA 209 9889*****************************************************..********** PP TIGR00507 207 gklvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdvekvfe 263 g +D+vy+ t+++++ +++ k +dGlgMlv+Qaa sF lw+gv pd v+ lcl|NCBI__GCF_000428045.1:WP_029134830.1 210 GGWTYDMVYASEPTAFVRWGQRHRaGKALDGLGMLVEQAAESFLLWRGVRPDTAPVIA 267 *******************9988869**************************998876 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: 8.61 // [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