Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_011372908.1 SUDEN_RS06690 shikimate dehydrogenase
Query= SwissProt::P56119 (263 letters) >NCBI__GCF_000012965.1:WP_011372908.1 Length = 263 Score = 200 bits (508), Expect = 3e-56 Identities = 112/254 (44%), Positives = 159/254 (62%), Gaps = 12/254 (4%) Query: 3 LKSFGVFGNPIKHSKSPLIHNACFLTFQKELRFLGHYHPILLPLESHIKSEFLHLGLSGA 62 +K F +FG+P+ HS+SPL+HN+ F K L + Y I L S +K FL L LSGA Sbjct: 1 MKLFAIFGDPVAHSRSPLMHNSVF----KNLNYKACYTRIHLQDGSKLKETFLSLKLSGA 56 Query: 63 NVTLPFKERAFQVCDKIKGIALECGAVNTLVLENDELVGYNTDALGFYLSLKQ-KNYQNA 121 N+T+P KE A+ CD+++G A + G VNT+V EN L+GYNTDA GF ++K+ + +N Sbjct: 57 NITVPHKEAAYAACDEVRGFAKKVGVVNTIVNENGRLIGYNTDADGFMFAIKEFGDVKNI 116 Query: 122 LILGAGGSAKALACELKKQGLQVSVLNRSSRGLDFFQRLGCDCF----MEPPKSAFDLII 177 LILGAGG+AKALA + G++VSV+NRS L +F+ LGC+CF E K +DL++ Sbjct: 117 LILGAGGTAKALASKFIDSGIKVSVMNRSDSRLSYFKELGCECFNWDNFEIKK--YDLVL 174 Query: 178 NATSASLHN-ELPLNKEVLKGYFKEGKLAYDLAYGFLTPFLSLAKELKTPFQDGKDMLIY 236 N+TSA L + E P +++ ++ YG +TPFL LAKE +DG DML+ Sbjct: 175 NSTSAGLKDKEFPAPLALIEQILNNTSFVAEVIYGKITPFLKLAKEKNITCKDGADMLLA 234 Query: 237 QAALSFEKFSASQI 250 Q L+ E F S++ Sbjct: 235 QGILANELFVNSEL 248 Lambda K H 0.322 0.139 0.408 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: 211 Number of extensions: 10 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: 263 Length of database: 263 Length adjustment: 25 Effective length of query: 238 Effective length of database: 238 Effective search space: 56644 Effective search space used: 56644 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 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_011372908.1 SUDEN_RS06690 (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.26708.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-69 219.5 0.1 2.6e-69 219.3 0.1 1.0 1 lcl|NCBI__GCF_000012965.1:WP_011372908.1 SUDEN_RS06690 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012965.1:WP_011372908.1 SUDEN_RS06690 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 219.3 0.1 2.6e-69 2.6e-69 1 263 [. 2 255 .. 2 262 .. 0.92 Alignments for each domain: == domain 1 score: 219.3 bits; conditional E-value: 2.6e-69 TIGR00507 1 kllgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevle 69 kl++++G+p++hS spl+hn ++k+l+ + Y++++ +++ +k ++++ +l l+G+n+TvP+Ke++++ lcl|NCBI__GCF_000012965.1:WP_011372908.1 2 KLFAIFGDPVAHSRSPLMHNSVFKNLNYKACYTRIH--LQDGSKLKETFLSLKLSGANITVPHKEAAYA 68 689*****************************9876..57889999*********************** PP TIGR00507 70 llDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlk 138 +De+ + ak++g vNT++ e+g+l+gynTD+ G++ ++++ +k ++li+GAGG aka+a ++ + lcl|NCBI__GCF_000012965.1:WP_011372908.1 69 ACDEVRGFAKKVGVVNTIVNENGRLIGYNTDADGFMFAIKEFGDVK---NILILGAGGTAKALASKFID 134 *****************************************77777...******************** PP TIGR00507 139 adkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeid..eaevkaellk 205 + +v+++NR+ ++ + ++elg++++ + ++ e kk+dl++n+tsagl+ + ++ +++l+ lcl|NCBI__GCF_000012965.1:WP_011372908.1 135 SGIKVSVMNRSDSRL----SYFKELGCECF-NWDNFEIKKYDLVLNSTSAGLKDKEFpaPLALIEQILN 198 ***********8886....99*****9986.559******************9876424667889**** PP TIGR00507 206 egklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfe 263 + ++v ++y ++ tp+lk+ak+k+ dG +Ml aQ+ l+ el+ +e + + + + lcl|NCBI__GCF_000012965.1:WP_011372908.1 199 NTSFVAEVIYGKI-TPFLKLAKEKNITCKDGADMLLAQGILANELFVNSELKSDDIEH 255 *************.********************************999865555544 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (263 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: 7.07 // [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