Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate WP_027720602.1 H589_RS0102675 shikimate dehydrogenase
Query= curated2:C6BUS3 (272 letters) >NCBI__GCF_000425265.1:WP_027720602.1 Length = 272 Score = 441 bits (1135), Expect = e-129 Identities = 211/272 (77%), Positives = 240/272 (88%) Query: 1 MDVFKPEKLFGIIGHPLGHTMSPLLHNWGFAEHKIPAVYMAWPTEPEKVESFMQTFRNLP 60 M VF PE+LFGIIGHPLGHTMSP LHNW F ++KIPAVYM WPT PEKV++FMQ+FRNLP Sbjct: 1 MSVFIPERLFGIIGHPLGHTMSPRLHNWAFEQYKIPAVYMTWPTAPEKVKNFMQSFRNLP 60 Query: 61 ISGASVTIPHKLSVMDYIDQLTERAESVGAVNTLYWDGDKIVGDNTDAAGVSEPLRPYSD 120 ISGASVTIPHKLSV++YIDQLT RA++VGAVNTLYW D IVGDNTD AGVSEPLRP+ Sbjct: 61 ISGASVTIPHKLSVINYIDQLTPRAKAVGAVNTLYWRNDHIVGDNTDTAGVSEPLRPHCS 120 Query: 121 QIKKALLIGAGGAARAAITGLQSLGIKEIFITNRTKSKADDLAAEFKISALDWDARGDQH 180 Q+KKALLIGAGGAARAAI GL+SL IKEIFITNRTKSKADDLA EFKIS +DWD RGDQH Sbjct: 121 QVKKALLIGAGGAARAAIYGLKSLNIKEIFITNRTKSKADDLAKEFKISVIDWDNRGDQH 180 Query: 181 LDLIVNSTSLGMSGKFEEINPMIMENQDKNTIIFDLVYNPLETVLIRKAKSKGCTVIHGI 240 DLIVNST+LGMSGKFE+INPMIM QD NTII+DLVYNPLET LI++A KGCT+IHGI Sbjct: 181 FDLIVNSTALGMSGKFEKINPMIMAEQDSNTIIYDLVYNPLETALIKEATEKGCTIIHGI 240 Query: 241 EMFVHQGLEQFRLWTGIKLDEKKARELLLEKL 272 EMF+HQG+EQF++WTG ++ + AR LL++ L Sbjct: 241 EMFLHQGIEQFKIWTGKNIEPQAARHLLMKHL 272 Lambda K H 0.318 0.136 0.403 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: 298 Number of extensions: 6 Number of successful extensions: 1 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: 272 Length of database: 272 Length adjustment: 25 Effective length of query: 247 Effective length of database: 247 Effective search space: 61009 Effective search space used: 61009 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_027720602.1 H589_RS0102675 (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.25488.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-79 251.1 0.0 6.1e-79 250.9 0.0 1.0 1 lcl|NCBI__GCF_000425265.1:WP_027720602.1 H589_RS0102675 shikimate dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000425265.1:WP_027720602.1 H589_RS0102675 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 250.9 0.0 6.1e-79 6.1e-79 2 266 .. 9 269 .. 8 272 .] 0.91 Alignments for each domain: == domain 1 score: 250.9 bits; conditional E-value: 6.1e-79 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 l+g+iG+p h +sp +hn a++q ++ +Y+ ++ +e+++++++ +++l+++G++vT+P+K +v+++ lcl|NCBI__GCF_000425265.1:WP_027720602.1 9 LFGIIGHPLGHTMSPRLHNWAFEQYKIPAVYMTWPTAPEKVKNFMQSFRNLPISGASVTIPHKLSVINY 77 79******************************************************************* PP TIGR00507 71 lDeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlk 138 +D+++++ak++gavNTl +++++vg+nTD G+ L+ s+ k++l+iGAGGaa+a++ L++ lcl|NCBI__GCF_000425265.1:WP_027720602.1 78 IDQLTPRAKAVGAVNTLYWRNDHIVGDNTDTAGVSEPLRPhCSQ---VKKALLIGAGGAARAAIYGLKS 143 ***************************************94444...569******************* PP TIGR00507 139 a.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeid..eaevkaell 204 ke+ i+NRt++ka +la++++ ++ ++ +++dli+n+t++g+sg+ + ++ + ae lcl|NCBI__GCF_000425265.1:WP_027720602.1 144 LnIKEIFITNRTKSKADDLAKEFKI----SVIDWDNRGDQHFDLIVNSTALGMSGKFEkiNPMIMAEQ- 207 94589******************98....566666888899**************9965455555554. PP TIGR00507 205 kegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealk 266 +++++++Dlvynplet+l+kea +kg+ +i G++M+ +Q+ +F++wtg +++ + +++ l lcl|NCBI__GCF_000425265.1:WP_027720602.1 208 DSNTIIYDLVYNPLETALIKEATEKGCTIIHGIEMFLHQGIEQFKIWTGKNIEPQAARHLLM 269 55669********************************************9988777766655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (272 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: 8.05 // [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