Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_028584122.1 G494_RS0108070 shikimate dehydrogenase
Query= SwissProt::Q58484 (282 letters) >NCBI__GCF_000429965.1:WP_028584122.1 Length = 277 Score = 191 bits (486), Expect = 1e-53 Identities = 117/285 (41%), Positives = 162/285 (56%), Gaps = 19/285 (6%) Query: 2 INAKTKVIGLIGHPVEHSFSPIMHNAAFKDKGLNYVYVAFDVLPENLKYVIDGAKALGIV 61 IN T++ ++G+PV HS SP MHNAAF G+N YV E++K +DG + LG Sbjct: 3 INGTTRLYAIVGNPVGHSLSPAMHNAAFAHLGINAAYVPIQA--EDIKATVDGLRQLGFC 60 Query: 62 GFNVTIPHKIEIMKYLDEIDKDAQLIGAVNTIKIEDGK-----AIGYNTDGIGARMALEE 116 G ++T+P K +M+++DE+D A IGAVNT+ G GYNTD +G+ AL + Sbjct: 61 GASITVPFKEGVMRWVDELDHTAIQIGAVNTLAFHRGSDQTIHCHGYNTDWVGSNRALAD 120 Query: 117 EIGRVKDKNIVIYGAGGAARAVAFELAKDN-NIIIANRTVEKAEALAKEIAEKLNKKFGE 175 + + + +I GAGGAA+AVAF L + IANRT +A LA E+ N E Sbjct: 121 HL-TLSGSSALILGAGGAAKAVAFGLVNAGVEVFIANRTHHRARQLANELG--CNAVALE 177 Query: 176 EVKFSGLDVDLDGVDIIINATPIGMYPNIDVEPIVKAEKLREDMVVMDLIYNPLETVLLK 235 D+ +I+IN T +GM P+ D E ++ L VVMD++Y PLET LL+ Sbjct: 178 -------DIGRLQCEILINTTSVGMAPH-DQECPIREALLPGFRVVMDIVYAPLETRLLR 229 Query: 236 EAKKVNAKTINGLGMLIYQGAVAFKIWTGVEPNIEVMKNAIIDKI 280 A+ I+GL ML YQGA FKIWTG EP EVM+ A+ + Sbjct: 230 AARACGCTVIDGLAMLHYQGAAQFKIWTGQEPPAEVMRQALFSAL 274 Lambda K H 0.318 0.139 0.385 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: 190 Number of extensions: 6 Number of successful extensions: 5 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: 282 Length of database: 277 Length adjustment: 26 Effective length of query: 256 Effective length of database: 251 Effective search space: 64256 Effective search space used: 64256 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 bits)
Align candidate WP_028584122.1 G494_RS0108070 (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.22288.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-80 254.0 0.0 8e-80 253.8 0.0 1.0 1 lcl|NCBI__GCF_000429965.1:WP_028584122.1 G494_RS0108070 shikimate dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429965.1:WP_028584122.1 G494_RS0108070 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 253.8 0.0 8e-80 8e-80 2 269 .. 9 274 .. 8 275 .. 0.94 Alignments for each domain: == domain 1 score: 253.8 bits; conditional E-value: 8e-80 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 l++++Gnp+ hS+sp++hnaa+++lg++ Y+ ++ e+++ +++g+++lg+ G+++TvPfKe v++ lcl|NCBI__GCF_000429965.1:WP_028584122.1 9 LYAIVGNPVGHSLSPAMHNAAFAHLGINAAYVP--IQAEDIKATVDGLRQLGFCGASITVPFKEGVMRW 75 79*****************************86..56789***************************** PP TIGR00507 71 lDeieesakligavNTlkledg.....klvgynTDgiGlvssLeklsklksekrvliiGAGGaakaval 134 +De++++a +igavNTl + g + gynTD +G +L +l + ++li+GAGGaakava+ lcl|NCBI__GCF_000429965.1:WP_028584122.1 76 VDELDHTAIQIGAVNTLAFHRGsdqtiHCHGYNTDWVGSNRALADHLTLS-GSSALILGAGGAAKAVAF 143 *****************9765523333467***************66777.9***************** PP TIGR00507 135 eLlkadkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkael 203 L++a+ ev iaNRt +a++la++l a+ le++ + +++in+ts+g+ ++ +e ++++ l lcl|NCBI__GCF_000429965.1:WP_028584122.1 144 GLVNAGVEVFIANRTHHRARQLANELGC----NAVALEDIGRLQCEILINTTSVGMAPHDQECPIREAL 208 ***********************99865....788888******************************* PP TIGR00507 204 lkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 l +v+D+vy+plet ll+ a+ g+ vidGl Ml +Q+a +F++wtg+ep+ e++++al ++l lcl|NCBI__GCF_000429965.1:WP_028584122.1 209 LPGFRVVMDIVYAPLETRLLRAARACGCTVIDGLAMLHYQGAAQFKIWTGQEPPAEVMRQALFSAL 274 ************************************************************998887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (277 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.51 // [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