Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate WP_012972631.1 AZL_RS00020 shikimate dehydrogenase
Query= curated2:Q2VYH4 (276 letters) >NCBI__GCF_000010725.1:WP_012972631.1 Length = 296 Score = 358 bits (918), Expect = e-103 Identities = 183/288 (63%), Positives = 207/288 (71%), Gaps = 13/288 (4%) Query: 1 MSGKARLAGVLGWPVSHSRSPRLHGFWLEQMGIDGAYLPLAVAPEHLETVIRALPRMGFA 60 +SGKAR+AGV+GWP+ HSRSPRLHGFWL IDGAY+PLAVAPE E IRALP +GF Sbjct: 7 ISGKARIAGVMGWPIGHSRSPRLHGFWLRHYSIDGAYVPLAVAPERAEQAIRALPALGFR 66 Query: 61 GANVTVPHKEAVMRLVDHLDPLARRIGAVNTLVVRQDGTLEGRNTDAYGFFENLRQGCPL 120 G NVTVP KE R VD LD ARR+GAVNT+VV +DG LEG NTD +GF ENLR P Sbjct: 67 GCNVTVPLKEIAFRSVDRLDETARRMGAVNTIVVAEDGALEGGNTDGFGFIENLRAEQPG 126 Query: 121 WEPTSGPAAVIGAGGAARAVVAALADAGVPEIRLANRSRERAATLAADLG---------- 170 W GPA VIGAGGAARAVV AL DAG PE+RL NR+R RA LAADL Sbjct: 127 WTAEQGPAVVIGAGGAARAVVVALLDAGAPEVRLVNRTRARAEELAADLAPALAPDLAAV 186 Query: 171 ---GPVTVVDWAERAESLEGCALLVNTTTLGMTGQSSLDLDLAALPTTSVVNDIVYVPLV 227 G VTVVDW R +L+G +LLVNTTT GM GQ +LDL L ALP +++VNDIVYVPL Sbjct: 187 GVTGRVTVVDWVSRETALDGASLLVNTTTQGMAGQPALDLSLRALPVSALVNDIVYVPLE 246 Query: 228 TDLLARATARGNPIVDGLGMLLHQAVPGFEAWFGQRPQVSDQLRAFVL 275 T LLA A RGNP+ G+GMLLHQA PGF+AWFG PQV+ +L VL Sbjct: 247 TPLLAEAGRRGNPVAGGIGMLLHQARPGFKAWFGVEPQVTPELTRVVL 294 Lambda K H 0.320 0.136 0.410 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: 306 Number of extensions: 9 Number of successful extensions: 2 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: 276 Length of database: 296 Length adjustment: 26 Effective length of query: 250 Effective length of database: 270 Effective search space: 67500 Effective search space used: 67500 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_012972631.1 AZL_RS00020 (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.24976.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-68 216.9 0.0 1.9e-68 216.5 0.0 1.0 1 lcl|NCBI__GCF_000010725.1:WP_012972631.1 AZL_RS00020 shikimate dehydrogen Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010725.1:WP_012972631.1 AZL_RS00020 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 216.5 0.0 1.9e-68 1.9e-68 2 260 .. 13 287 .. 12 294 .. 0.93 Alignments for each domain: == domain 1 score: 216.5 bits; conditional E-value: 1.9e-68 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 + gv+G pi hS sp +h l++ +++ Y+ + v +e+ e+a+ ++ alg++G+nvTvP+Ke +++ lcl|NCBI__GCF_000010725.1:WP_012972631.1 13 IAGVMGWPIGHSRSPRLHGFWLRHYSIDGAYVPLAVAPERAEQAIRALPALGFRGCNVTVPLKEIAFRS 81 679****************************************************************** PP TIGR00507 71 lDeieesakligavNTlk.ledgklvgynTDgiGlvssLek..lsklksekrvliiGAGGaakavaleL 136 +D+++e+a+ +gavNT++ edg l+g nTDg G++ +L+ + ++ +++iGAGGaa+av+++L lcl|NCBI__GCF_000010725.1:WP_012972631.1 82 VDRLDETARRMGAVNTIVvAEDGALEGGNTDGFGFIENLRAeqPGWTAEQGPAVVIGAGGAARAVVVAL 150 *****************9899******************8863467777778***************** PP TIGR00507 137 lka.dkeviiaNRtvekaeelaerlqe...........lgei..lalsleevelkkvdliinatsagls 191 l+a ev ++NRt ++aeela l+ +g + + + e l+ +l++n+t g+ lcl|NCBI__GCF_000010725.1:WP_012972631.1 151 LDAgAPEVRLVNRTRARAEELAADLAPalapdlaavgvTGRVtvVDWVSRETALDGASLLVNTTTQGMA 219 ***6679***************999988999****999665511556678899999************* PP TIGR00507 192 geideaevkaellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvek 260 g+ ++ l ++lv D+vy pletpll+ea ++g +v+ G+gMl +Qa F+ w+gvep+v lcl|NCBI__GCF_000010725.1:WP_012972631.1 220 GQP-ALDLSLRALPVSALVNDIVYVPLETPLLAEAGRRGNPVAGGIGMLLHQARPGFKAWFGVEPQVTP 287 *98.788889999999*************************************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (296 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.93 // [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