Align Shikimate dehydrogenase (NADP(+)); SD; SDH; EC 1.1.1.25 (characterized)
to candidate WP_028950498.1 Q385_RS0104370 shikimate dehydrogenase
Query= SwissProt::O67049 (269 letters) >NCBI__GCF_000619805.1:WP_028950498.1 Length = 279 Score = 266 bits (681), Expect = 3e-76 Identities = 130/276 (47%), Positives = 193/276 (69%), Gaps = 12/276 (4%) Query: 1 MINAQTQLYGVIGFPVKHSLSPVFQNALIRYAGLNAVYLAFEINPEELKKAFEGFKALKV 60 +++ QT++YG+ G+PVKHS SP FQ A Y G+NAVY+ FE+NP++L+KA E K LK+ Sbjct: 2 ILDGQTKVYGIFGYPVKHSKSPTFQTAAFLYLGINAVYVPFEVNPDDLEKAVESLKVLKI 61 Query: 61 KGINVTVPFKEEIIPLLDYVEDTAKEIGAVNTVKFENGKAYGYNTDWIGFLKSLKSLIPE 120 G+N+T+P KE +I ++ + + K I A NT+K +G YNTDWIGF++ LK L P Sbjct: 62 AGVNITIPHKENVINYVNELSEEVKVIKAANTIKNVDGYLIAYNTDWIGFIEGLKELEPN 121 Query: 121 VKEKSILVLGAGGASRAVIYALVKEGA-KVFLWNRTKEKAIKLAQKFP-----LEVVNSP 174 ++ K +LV+GAGG+SRA+IY L+KE K++L NRT ++A KL Q++ ++ + +P Sbjct: 122 LEGKKVLVIGAGGSSRAIIYGLLKENVDKIYLANRTLQRAEKLIQEYKEYFRIVDKIITP 181 Query: 175 ------EEVIDKVQVIVNTTSVGLKDKDPEIFNYDLIKKDHVVVDIIYKETKLLKKAKEK 228 E + V +IVNTTSVGL ++D +F+Y+++K+ VVDIIYKETKLLK AKEK Sbjct: 182 ISLQDIETFLSDVDIIVNTTSVGLNNEDFPLFDYNILKESQTVVDIIYKETKLLKAAKEK 241 Query: 229 GAKLFDGLPMLLWQGIEAFKIWNGCEVPYSVAERSV 264 G K +G PML++QG ++F+IW G + P V ++S+ Sbjct: 242 GCKYQNGFPMLIYQGAKSFEIWTGQKAPVEVMKKSL 277 Lambda K H 0.318 0.138 0.396 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: 269 Number of extensions: 11 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: 269 Length of database: 279 Length adjustment: 25 Effective length of query: 244 Effective length of database: 254 Effective search space: 61976 Effective search space used: 61976 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_028950498.1 Q385_RS0104370 (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.23227.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-81 259.0 0.1 2.4e-81 258.8 0.1 1.0 1 lcl|NCBI__GCF_000619805.1:WP_028950498.1 Q385_RS0104370 shikimate dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000619805.1:WP_028950498.1 Q385_RS0104370 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 258.8 0.1 2.4e-81 2.4e-81 1 264 [. 8 276 .. 8 278 .. 0.94 Alignments for each domain: == domain 1 score: 258.8 bits; conditional E-value: 2.4e-81 TIGR00507 1 kllgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevle 69 k++g++G+p+khSksp + aa+ lg++ +Y+ fev++++leka++ +k l + Gvn+T+P+Ke+v++ lcl|NCBI__GCF_000619805.1:WP_028950498.1 8 KVYGIFGYPVKHSKSPTFQTAAFLYLGINAVYVPFEVNPDDLEKAVESLKVLKIAGVNITIPHKENVIN 76 68******************************************************************* PP TIGR00507 70 llDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlk 138 ++ e++e++k+i+a NT+k dg l++ynTD iG++ L++l++ ++k+vl+iGAGG+++a++ Llk lcl|NCBI__GCF_000619805.1:WP_028950498.1 77 YVNELSEEVKVIKAANTIKNVDGYLIAYNTDWIGFIEGLKELEPNLEGKKVLVIGAGGSSRAIIYGLLK 145 *****************************************988888*******************999 PP TIGR00507 139 a.dkeviiaNRtvekaeelaerlqe.....lgeilalsleeve..lkkvdliinatsaglsgeideaev 199 + ++ +aNRt+++ae+l+++ +e + i+ +sl+++e l+ vd+i+n+ts+gl++e + lcl|NCBI__GCF_000619805.1:WP_028950498.1 146 EnVDKIYLANRTLQRAEKLIQEYKEyfrivDKIITPISLQDIEtfLSDVDIIVNTTSVGLNNED-FPLF 213 84579*******************977765456667889888833566************9987.7889 PP TIGR00507 200 kaellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfea 264 + ++lke++ vvD++y+ et llk ak+kg+k ++G+ Ml++Q+a+sFe+wtg++ +ve++++ lcl|NCBI__GCF_000619805.1:WP_028950498.1 214 DYNILKESQTVVDIIYK--ETKLLKAAKEKGCKYQNGFPMLIYQGAKSFEIWTGQKAPVEVMKKS 276 9***************7..67*****************************************986 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: 7.57 // [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