Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_073036355.1 BUB04_RS01740 shikimate dehydrogenase
Query= BRENDA::O27957 (269 letters) >NCBI__GCF_900129305.1:WP_073036355.1 Length = 275 Score = 169 bits (428), Expect = 6e-47 Identities = 113/273 (41%), Positives = 155/273 (56%), Gaps = 22/273 (8%) Query: 5 GVIGYPIKHSVSPAMHNAALQHEGIEGIYLAFEVKPDRLRDAVFGAKALGFRGLNVTIPF 64 GVIG P++HS+SPAM NAAL H GI YLA E D R + K +G RGL+VTIP+ Sbjct: 11 GVIGSPVRHSLSPAMMNAALAHLGIPAFYLALE--SDDFRSDLEILKRMGVRGLSVTIPY 68 Query: 65 KESVVEFVELEGEAA-KIKTVNTIDLVEMV--GYNTDVYG-VKAALSGTELGGKTALVVG 120 KE + EAA I VNT+ + G NTD G V+A + TE+ G+ ALV+G Sbjct: 69 KEDAFRWCASVDEAAYAIGAVNTLRCTDGAWEGINTDWIGAVRALETATEIRGRKALVLG 128 Query: 121 AGGAGKAAALALLDMGSTVIVANRTEEKGREAVEMLRRYGECIFWPLSRVEELKGKVDVV 180 AGGA K AL+ G+ V+VANRTE K R ++ RR+G C + PL R+ L ++D+ Sbjct: 129 AGGAAKGVVYALVRSGAQVVVANRTEGKAR---DLARRFG-CDWIPLDRMRGL--EIDMA 182 Query: 181 VNATPLGMRG----FKAE-IPVPPSMLDGVELVFDTVYNPMETPLIREAKKRGCKVVYGI 235 V+ T GM G F E +P+ P + + D VY P++TP + A+ +G + G+ Sbjct: 183 VHCTAGGMHGRPYAFSLEDVPIRPGV-----VAMDIVYAPLKTPFLEAARAKGALSLDGL 237 Query: 236 EMLVHQGAKAFEIWTGIEPDVGVMREAALRALR 268 EML+HQG + W G VMR A +A + Sbjct: 238 EMLLHQGVEQLTWWLGRPAPASVMRHALRKAAK 270 Lambda K H 0.320 0.139 0.401 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: 215 Number of extensions: 10 Number of successful extensions: 4 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: 275 Length adjustment: 25 Effective length of query: 244 Effective length of database: 250 Effective search space: 61000 Effective search space used: 61000 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_073036355.1 BUB04_RS01740 (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.32431.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-71 226.9 0.0 1.5e-71 226.7 0.0 1.0 1 lcl|NCBI__GCF_900129305.1:WP_073036355.1 BUB04_RS01740 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900129305.1:WP_073036355.1 BUB04_RS01740 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 226.7 0.0 1.5e-71 1.5e-71 2 268 .. 9 268 .. 8 270 .. 0.97 Alignments for each domain: == domain 1 score: 226.7 bits; conditional E-value: 1.5e-71 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 l+gviG p++hS+sp++ naal++lg+ Yla+e +++++ l+ +k g++G++vT+P+Ke +++ lcl|NCBI__GCF_900129305.1:WP_073036355.1 9 LYGVIGSPVRHSLSPAMMNAALAHLGIPAFYLALE--SDDFRSDLEILKRMGVRGLSVTIPYKEDAFRW 75 79*****************************9975..689***************************** PP TIGR00507 71 lDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka 139 + ++e a +igavNTl+ dg +g nTD iG+v +Le ++++ ++++l++GAGGaak+v+ +L++ lcl|NCBI__GCF_900129305.1:WP_073036355.1 76 CASVDEAAYAIGAVNTLRCTDGAWEGINTDWIGAVRALETATEIR-GRKALVLGAGGAAKGVVYALVRS 143 *********************************************.*********************** PP TIGR00507 140 dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegk 208 + +v++aNRt+ ka++la r+ ++l++++ ++d+ +++t+ g++g +++ ++ g lcl|NCBI__GCF_900129305.1:WP_073036355.1 144 GAQVVVANRTEGKARDLARRFGC----DWIPLDRMRGLEIDMAVHCTAGGMHGRPYAFSLEDVPIRPGV 208 *****************988765....68999**********************999************ PP TIGR00507 209 lvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealkek 268 +++D+vy+pl+tp+l+ a+ kg+ +dGl+Ml +Q++ + w g + +++++al+++ lcl|NCBI__GCF_900129305.1:WP_073036355.1 209 VAMDIVYAPLKTPFLEAARAKGALSLDGLEMLLHQGVEQLTWWLGRPAPASVMRHALRKA 268 ******************************************************999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (275 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: 00:00:00.00 # Mc/sec: 8.89 // [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