Align quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate WP_012334470.1 M446_RS22840 shikimate dehydrogenase
Query= BRENDA::Q9X5C9 (283 letters) >NCBI__GCF_000019365.1:WP_012334470.1 Length = 285 Score = 212 bits (539), Expect = 9e-60 Identities = 126/275 (45%), Positives = 167/275 (60%), Gaps = 8/275 (2%) Query: 6 LLGLIGQGLDLSRTPAMHEAEGLAQGRATVYRRIDTLGSRASGQDLKTLLDAALYLGFNG 65 LLGLIG + S +PAMHEA A G Y+ I+ G+ A L++LLD +LGF G Sbjct: 10 LLGLIGAPIKHSASPAMHEAAAEALGMRAHYQLIEIAGADAGL--LRSLLDGVRHLGFAG 67 Query: 66 LNITHPYKQAVLPLLDEVSEQATQLGAVNTVVIDATGHTTGHNTDVSGFGRGMEEGLPNA 125 +N+T PYK+AVLPLLD++S A +GAVNTVV++ G GHNTD SGFGR + + A Sbjct: 68 VNVTFPYKEAVLPLLDDLSPGARAVGAVNTVVVEG-GRLIGHNTDASGFGRALVQTFGPA 126 Query: 126 KLDSVVQVGAGGVGNAVAYALVTHGVQKLQVADLDTSRAQALADVINNAVGREAVVGVDA 185 V +GAGGVG A+A AL ++++ D D ++A+ALA ++ A + V A Sbjct: 127 PAGPVALIGAGGVGKAIAVALSDVPGTEIRLVDTDPAKARALAASLDG----RAEIRVCA 182 Query: 186 RGIEDVIAAADGVVNATPMGMPAHPGTAFDVSCLTKDHWVGDVVYMPIETELLKAARALG 245 G E+ +A A G+VN TP+GM + + L D WV D VY P+ T LL AARALG Sbjct: 183 -GAEEALAGARGLVNGTPIGMLPNRDAPVPLHLLRPDLWVADAVYSPLWTPLLTAARALG 241 Query: 246 CETLDGTRMAIHQAVDAFRLFTGLEPDVSRMRETF 280 T+ G +AIHQA+DAFRLFTG E + M F Sbjct: 242 APTMTGRALAIHQALDAFRLFTGREAPQAAMERAF 276 Lambda K H 0.318 0.135 0.384 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: 231 Number of extensions: 16 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: 283 Length of database: 285 Length adjustment: 26 Effective length of query: 257 Effective length of database: 259 Effective search space: 66563 Effective search space used: 66563 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_012334470.1 M446_RS22840 (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.399.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-64 203.8 0.0 1.7e-64 203.5 0.0 1.0 1 lcl|NCBI__GCF_000019365.1:WP_012334470.1 M446_RS22840 shikimate dehydroge Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019365.1:WP_012334470.1 M446_RS22840 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 203.5 0.0 1.7e-64 1.7e-64 2 264 .. 10 275 .. 9 282 .. 0.95 Alignments for each domain: == domain 1 score: 203.5 bits; conditional E-value: 1.7e-64 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveiee...lekalsgikalglkGvnvTvPfKeev 67 llg+iG pikhS sp++h+aa++ lg+ +Y +e+ + l++ l+g+++lg+ GvnvT P+Ke+v lcl|NCBI__GCF_000019365.1:WP_012334470.1 10 LLGLIGAPIKHSASPAMHEAAAEALGMRAHYQLIEIAGADaglLRSLLDGVRHLGFAGVNVTFPYKEAV 78 68*****************************9999877666779************************* PP TIGR00507 68 lellDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleL 136 l+llD++++ a+++gavNT+++e+g+l+g+nTD+ G+ +L + + + v++iGAGG +ka+a++L lcl|NCBI__GCF_000019365.1:WP_012334470.1 79 LPLLDDLSPGARAVGAVNTVVVEGGRLIGHNTDASGFGRALVQTFGPAPAGPVALIGAGGVGKAIAVAL 147 *******************************************888889******************** PP TIGR00507 137 lka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaell 204 ++ ++e+ ++ +ka++la l ei +e l ++n t++g+ ++ +a+v+ +ll lcl|NCBI__GCF_000019365.1:WP_012334470.1 148 SDVpGTEIRLVDTDPAKARALAASLDGRAEIRVCAGAEEALAGARGLVNGTPIGMLPNR-DAPVPLHLL 215 **989******************************************************.9******** PP TIGR00507 205 kegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfea 264 + + v D vy pl tpll a+ +g++++ G + ++Qa+ +F+l+tg e + + +a lcl|NCBI__GCF_000019365.1:WP_012334470.1 216 RPDLWVADAVYSPLWTPLLTAARALGAPTMTGRALAIHQALDAFRLFTGREAPQAAMERA 275 **************************************************9665555444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (285 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: 9.65 // [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