Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate WP_011159859.1 TX73_RS22045 shikimate dehydrogenase (NADP+)
Query= reanno::Caulo:CCNA_00003 (285 letters) >NCBI__GCF_000195775.1:WP_011159859.1 Length = 278 Score = 189 bits (481), Expect = 4e-53 Identities = 113/262 (43%), Positives = 152/262 (58%), Gaps = 3/262 (1%) Query: 16 GQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRGGAVRGLNVTIPFKER 75 G P HS SP+IH+ W+ G++ Y A + F FV L+ G NVTIP KER Sbjct: 12 GCPAAHSRSPLIHHYWLRQLGIEGGYSIEAVPPEGFAEFVLHLKTHGYVGANVTIPHKER 71 Query: 76 ALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAIQAPGFDVTAAPVVIL 135 AL + + + A GAAN L ++ D + + NTD G +G + APG+D +A ++L Sbjct: 72 ALQLTEP-DERACAVGAANTLYYDGD-LLRSTNTDIEGFIGNLDASAPGWD-RSAHALVL 128 Query: 136 GAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAKGEDALPALLPEAGLI 195 GAGG++R V LL G RIA+ NR++ RAQ L D FGE+VV +PA LP AGL+ Sbjct: 129 GAGGSSRAVVFGLLERGVQRIALANRSIERAQALRDLFGERVVPIAWSDIPAALPGAGLL 188 Query: 196 INATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEAAGRRTVDGLEMLLRQ 255 +N TSLG+ G DL+ P AVV D+VY PL T+ L A+A G RT DGL MLL Q Sbjct: 189 VNTTSLGMKGQPPLQIDLSALPADAVVSDLVYVPLETDLLAAAKARGLRTADGLGMLLHQ 248 Query: 256 AIPTFETIYGQAPSPKIDVRVL 277 A+ F+ +G P ++R L Sbjct: 249 AVRGFDLWFGARPHVTPELRAL 270 Lambda K H 0.319 0.136 0.390 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: 213 Number of extensions: 9 Number of successful extensions: 3 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: 285 Length of database: 278 Length adjustment: 26 Effective length of query: 259 Effective length of database: 252 Effective search space: 65268 Effective search space used: 65268 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_011159859.1 TX73_RS22045 (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.14438.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.5e-66 207.7 0.0 1.2e-65 207.4 0.0 1.0 1 lcl|NCBI__GCF_000195775.1:WP_011159859.1 TX73_RS22045 shikimate dehydroge Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195775.1:WP_011159859.1 TX73_RS22045 shikimate dehydrogenase (NADP+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 207.4 0.0 1.2e-65 1.2e-65 4 263 .. 9 268 .. 6 274 .. 0.94 Alignments for each domain: == domain 1 score: 207.4 bits; conditional E-value: 1.2e-65 TIGR00507 4 gviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellD 72 +iG p +hS splih l+qlg+e+ Y v++e + +++ +k+ g G+nvT+P+Ke++l+l lcl|NCBI__GCF_000195775.1:WP_011159859.1 9 CLIGCPAAHSRSPLIHHYWLRQLGIEGGYSIEAVPPEGFAEFVLHLKTHGYVGANVTIPHKERALQLT- 76 69*****************************************************************9. PP TIGR00507 73 eieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka. 139 e +e+a ++ga NTl +++ l + nTD +G++ +L ++l++GAGG+++av++ Ll+ lcl|NCBI__GCF_000195775.1:WP_011159859.1 77 EPDERACAVGAANTLYYDGDLLRSTNTDIEGFIGNLDAsAPGWDRSAHALVLGAGGSSRAVVFGLLERg 145 9************************************9655556699******************9995 PP TIGR00507 140 dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegk 208 +++ +aNR+ e+a++l + + e +a+s l l++n+ts+g++g+ +++ + l +++ lcl|NCBI__GCF_000195775.1:WP_011159859.1 146 VQRIALANRSIERAQALRDLFGERVVPIAWSDIPAALPGAGLLVNTTSLGMKGQP-PLQIDLSALPADA 213 688********************8888888877777778**************98.899********** PP TIGR00507 209 lvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfe 263 +v Dlvy plet ll+ ak +g +++dGlgMl +Qa+ F lw+g p+v + lcl|NCBI__GCF_000195775.1:WP_011159859.1 214 VVSDLVYVPLETDLLAAAKARGLRTADGLGMLLHQAVRGFDLWFGARPHVTPELR 268 *************************************************987655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (278 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: 00:00:00.01 # Mc/sec: 6.58 // [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