Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate WP_013553651.1 NITSA_RS03505 shikimate dehydrogenase
Query= curated2:Q7VGS3 (268 letters) >NCBI__GCF_000186245.1:WP_013553651.1 Length = 266 Score = 211 bits (536), Expect = 2e-59 Identities = 114/263 (43%), Positives = 156/263 (59%), Gaps = 8/263 (3%) Query: 5 FAVYGNPITHSKSPFLHNYAFTKLGLSGYYSRILLDKGANLRQNFLSNGLSGANITLPFK 64 FA++GNP+ HS+SP +HNY F L Y R L++G LR+ FL GL GANIT+P K Sbjct: 6 FAIFGNPVAHSRSPLMHNYTFQTLDYPACYGRYRLEEGERLREVFLKLGLKGANITVPHK 65 Query: 65 EEAFNQCDEVRGVAQNIGACNTWVLEDKNHLVGYNTDAQGFYECIKEY-KIKNALIIGAG 123 E A+ CDE+ A+ +GA NT VL D L GYNTDA GF ++E+ K L +GAG Sbjct: 66 EHAYRACDELDDFARKVGAVNTIVLRD-GKLHGYNTDAPGFLRVVEEFGGGKRVLFLGAG 124 Query: 124 GSAKAVAMILQSHNIPTTLINRSVQNLSFFVHKGFECYVNSEFKPTCSYDILINTTSAGL 183 G+A + AMIL+ T++NRS L F +GF Y EF P +YD+++N +SAGL Sbjct: 125 GTAASTAMILREAGYEVTILNRSAGRLESFKEQGFAAYTWEEFAPG-AYDLIVNMSSAGL 183 Query: 184 NDNLLPCDESQLKELCSCGKYAFDLIYGKCTPFLALAQSFHLSCSDGKEMLINQAALSFE 243 D LP L+ L A D+IYGK TPFL LA+S + DG EML+ Q ++F+ Sbjct: 184 EDESLPAPREILEPLLRRASGALDVIYGKETPFLRLARSLGVRSKDGSEMLLYQGVIAFD 243 Query: 244 LFCKQKYNKGNLEIQRIASFMNE 266 F +G+ ++++I M E Sbjct: 244 YF-----TEGHFDLEKIEKAMRE 261 Lambda K H 0.322 0.137 0.415 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: 200 Number of extensions: 8 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 268 Length of database: 266 Length adjustment: 25 Effective length of query: 243 Effective length of database: 241 Effective search space: 58563 Effective search space used: 58563 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_013553651.1 NITSA_RS03505 (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.11129.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-67 211.4 0.0 7.8e-67 211.2 0.0 1.0 1 lcl|NCBI__GCF_000186245.1:WP_013553651.1 NITSA_RS03505 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013553651.1 NITSA_RS03505 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 211.2 0.0 7.8e-67 7.8e-67 2 268 .. 5 262 .. 4 264 .. 0.92 Alignments for each domain: == domain 1 score: 211.2 bits; conditional E-value: 7.8e-67 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 l++++Gnp++hS spl+hn ++++l+ Y + +e+ e+ + + +lglkG+n+TvP+Ke++++ lcl|NCBI__GCF_000186245.1:WP_013553651.1 5 LFAIFGNPVAHSRSPLMHNYTFQTLDYPACYGRYRLEEG--ERLREVFLKLGLKGANITVPHKEHAYRA 71 79******************************9988765..455566899******************* PP TIGR00507 71 lDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka 139 +De+++ a+++gavNT++l+dgkl gynTD+ G++ + e+ +krvl +GAGG a + a+ L +a lcl|NCBI__GCF_000186245.1:WP_013553651.1 72 CDELDDFARKVGAVNTIVLRDGKLHGYNTDAPGFLRVVEE---FGGGKRVLFLGAGGTAASTAMILREA 137 *************************************999...67799********************* PP TIGR00507 140 dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeid..eaevkaellke 206 + ev+i+NR+ + e ++e g a ee + +dli+n sagl+ e e+ + ll+ lcl|NCBI__GCF_000186245.1:WP_013553651.1 138 GYEVTILNRSAGRL----ESFKEQG-FAAYTWEEFAPGAYDLIVNMSSAGLEDESLpaPREILEPLLRR 201 **********5554....6666645.456667899****************988643577899999*** PP TIGR00507 207 gklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealkek 268 + ++D++y + tp+l++a+++g + dG +Ml +Q++ +F +t + d+ek+ +a++e lcl|NCBI__GCF_000186245.1:WP_013553651.1 202 ASGALDVIYGKE-TPFLRLARSLGVRSKDGSEMLLYQGVIAFDYFTEGHFDLEKIEKAMRES 262 **********97.********************************************99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (266 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.34 // [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