Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_086508114.1 BZY95_RS00850 shikimate dehydrogenase
Query= BRENDA::Q88RQ5 (274 letters) >NCBI__GCF_002151265.1:WP_086508114.1 Length = 279 Score = 300 bits (768), Expect = 2e-86 Identities = 162/276 (58%), Positives = 193/276 (69%), Gaps = 9/276 (3%) Query: 2 DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGS-GGNVT 60 DQY VFGNPI HSKSPLIH FA QTG+ LEY + APLD+F+ + F QG G NVT Sbjct: 3 DQYCVFGNPISHSKSPLIHAAFAAQTGEALEYTAIEAPLDDFAGTWQRFVAQGGRGANVT 62 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTL-----SKLADGTLQGDNTDGAGLVRDLTVNAGV 115 VPFKEEAFRLCD+L+ RARRAGAVNTL + D + GD TDG GLVRDL + GV Sbjct: 63 VPFKEEAFRLCDTLSRRARRAGAVNTLVLGKNGQRNDFKIYGDTTDGVGLVRDLE-HHGV 121 Query: 116 ELAGKRILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFA 175 L G RIL+LGAGGAVRGVLEP+LA +P + +ANRT KA LA +F +LG + GF Sbjct: 122 ALEGARILVLGAGGAVRGVLEPLLATRPARVQVANRTAAKAAALAEDFADLGEIHGGGFD 181 Query: 176 WLQEPVDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKV 235 + P D+++N TSASL+G+LPP+ D L G T YDMMYG EPT F +WA G A+ Sbjct: 182 EVSGPFDLVVNGTSASLSGDLPPLPDDLFAEGAT-AYDMMYGAEPTVFLRWAQARG-ARG 239 Query: 236 LDGLGMLAEQAAEAFFIWRGVRPDTAPVLAELRRQL 271 +DGLGML EQAAE+FF+WR RP+T PV LR L Sbjct: 240 IDGLGMLVEQAAESFFLWRNKRPETGPVRERLRHLL 275 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: 288 Number of extensions: 17 Number of successful extensions: 6 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: 279 Length adjustment: 25 Effective length of query: 249 Effective length of database: 254 Effective search space: 63246 Effective search space used: 63246 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_086508114.1 BZY95_RS00850 (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.19569.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-81 257.8 0.0 5.7e-81 257.6 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508114.1 BZY95_RS00850 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508114.1 BZY95_RS00850 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.6 0.0 5.7e-81 5.7e-81 2 269 .. 4 275 .. 3 276 .. 0.94 Alignments for each domain: == domain 1 score: 257.6 bits; conditional E-value: 5.7e-81 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 + v+Gnpi hSksplih a+++q+g +leY+a+e++++++ + + + a+g +G+nvTvPfKee+++l lcl|NCBI__GCF_002151265.1:WP_086508114.1 4 QYCVFGNPISHSKSPLIHAAFAAQTGEALEYTAIEAPLDDFAGTWQRFVAQGGRGANVTVPFKEEAFRL 72 589****************************************************************** PP TIGR00507 71 lDeieesakligavNTlkl.edg.....klvgynTDgiGlvssLeklsklksekrvliiGAGGaakava 133 +D ++++a+ +gavNTl+l ++g k++g+ TDg+Glv +Le+ ++ r+l++GAGGa ++v+ lcl|NCBI__GCF_002151265.1:WP_086508114.1 73 CDTLSRRARRAGAVNTLVLgKNGqrndfKIYGDTTDGVGLVRDLEHHGVALEGARILVLGAGGAVRGVL 141 *****************973222333349*****************666666***************** PP TIGR00507 134 leLlka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevka 201 +Ll + + +v +aNRt +ka +lae ++ lgei +ev +dl++n tsa+lsg++ ++++ lcl|NCBI__GCF_002151265.1:WP_086508114.1 142 EPLLATrPARVQVANRTAAKAAALAEDFADLGEIHGGGFDEVSG-PFDLVVNGTSASLSGDL--PPLPD 207 **998879****************************99999875.6****************..***** PP TIGR00507 202 ellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 +l++eg+ ++D++y t++l++a+ +g++ idGlgMlv+Qaa sF lw+ p+ v+e+l++ l lcl|NCBI__GCF_002151265.1:WP_086508114.1 208 DLFAEGATAYDMMYGAEPTVFLRWAQARGARGIDGLGMLVEQAAESFFLWRNKRPETGPVRERLRHLL 275 **************************************************************998765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (279 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.51 // [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