Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_013682880.1 ARCVE_RS00800 shikimate dehydrogenase
Query= BRENDA::O27957 (269 letters) >NCBI__GCF_000194625.1:WP_013682880.1 Length = 271 Score = 335 bits (860), Expect = 5e-97 Identities = 167/266 (62%), Positives = 213/266 (80%), Gaps = 3/266 (1%) Query: 5 GVIGYPIKHSVSPAMHNAALQHEGIEGIYLAFEVKPDRLRDAVFGAKALGFRGLNVTIPF 64 GVIGYPIKHSVSPAMHNAA + GI+ IYLAFEV+P+ LRDAVFGAKALG RGLNVTIP Sbjct: 5 GVIGYPIKHSVSPAMHNAAFRRLGIDAIYLAFEVRPESLRDAVFGAKALGIRGLNVTIPH 64 Query: 65 KESVVEFVELEGEAAKIKTVNTIDLVEMVGYNTDVYGVKAALSGTELG--GKTALVVGAG 122 KE +++FV+ G AAKI VNT+ + + G+NTD YG AL +G GKTAL+VGAG Sbjct: 65 KEEILKFVKPVGIAAKIGAVNTVVVDRLEGHNTDAYGAMKALENAGVGVEGKTALLVGAG 124 Query: 123 GAGKAAALALLDMGSTVIVANRTEEKGREAVEMLRRYGECIFWPLSRVEELKGKVDVVVN 182 GA +A A AL++ G+TVIV NRTE KG + VE +R+ GECIF+P R+EELKGK+D+++N Sbjct: 125 GAARAIAFALVENGATVIVTNRTESKGLKLVEDVRKSGECIFYPYDRLEELKGKIDIIIN 184 Query: 183 ATPLGMRGFKAEIPVPPSMLDGVELVFDTVYNPMETPLIREAKKRGCKVVYGIEMLVHQG 242 ATPLGM+GF++++PVP ++D V +VFDTVYNPMET LI AK+RGC+VVYGI+MLV QG Sbjct: 185 ATPLGMKGFESKLPVPEGLVDDV-VVFDTVYNPMETLLISLAKRRGCRVVYGIDMLVFQG 243 Query: 243 AKAFEIWTGIEPDVGVMREAALRALR 268 A+AF +W ++P V VM++AA+ AL+ Sbjct: 244 AEAFRLWLDVDPPVDVMKKAAIDALK 269 Lambda K H 0.320 0.139 0.401 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: 282 Number of extensions: 9 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: 269 Length of database: 271 Length adjustment: 25 Effective length of query: 244 Effective length of database: 246 Effective search space: 60024 Effective search space used: 60024 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_013682880.1 ARCVE_RS00800 (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.27852.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-95 302.9 0.0 9.4e-95 302.8 0.0 1.0 1 lcl|NCBI__GCF_000194625.1:WP_013682880.1 ARCVE_RS00800 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000194625.1:WP_013682880.1 ARCVE_RS00800 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 302.8 0.0 9.4e-95 9.4e-95 2 269 .. 3 268 .. 2 269 .. 0.97 Alignments for each domain: == domain 1 score: 302.8 bits; conditional E-value: 9.4e-95 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 ++gviG+pikhS+sp++hnaa++ lg++ Ylafev++e+l++a++g+kalg++G+nvT+P+Kee+l++ lcl|NCBI__GCF_000194625.1:WP_013682880.1 3 CYGVIGYPIKHSVSPAMHNAAFRRLGIDAIYLAFEVRPESLRDAVFGAKALGIRGLNVTIPHKEEILKF 71 79******************************************************************* PP TIGR00507 71 lDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka 139 + + + a++igavNT++++ l+g+nTD++G++++Le+ ++k++l++GAGGaa+a+a++L+++ lcl|NCBI__GCF_000194625.1:WP_013682880.1 72 V-KPVGIAAKIGAVNTVVVDR--LEGHNTDAYGAMKALENAGVGVEGKTALLVGAGGAARAIAFALVEN 137 *.999************9865..*****************666666*********************** PP TIGR00507 140 dkeviiaNRtvekaeelaerlqelgeilalsleevelkk..vdliinatsaglsgeideaevkaellke 206 + +vi++NRt++k+ +l+e +++ ge+++ + +++e+ k +d+iinat++g++g ++ +v+++l++ lcl|NCBI__GCF_000194625.1:WP_013682880.1 138 GATVIVTNRTESKGLKLVEDVRKSGECIFYPYDRLEELKgkIDIIINATPLGMKGFESKLPVPEGLVDD 206 ***********************************998889****************9*****999888 PP TIGR00507 207 gklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 +v+D+vynp+et l+++ak++g++v++G++Mlv Q+a +F+lw v p+v+++++a++++l lcl|NCBI__GCF_000194625.1:WP_013682880.1 207 V-VVFDTVYNPMETLLISLAKRRGCRVVYGIDMLVFQGAEAFRLWLDVDPPVDVMKKAAIDAL 268 7.********************************************************99988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (271 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: 7.96 // [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