Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate WP_043745705.1 AMB_RS23010 shikimate dehydrogenase
Query= reanno::Caulo:CCNA_00003 (285 letters) >NCBI__GCF_000009985.1:WP_043745705.1 Length = 278 Score = 199 bits (506), Expect = 6e-56 Identities = 111/275 (40%), Positives = 146/275 (53%) Query: 5 ITGAAIVGGVCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRGGAVR 64 ++G A + GV G P+ HS SP +H W+ G+D AY+P A A + ET + L Sbjct: 3 VSGKARLAGVLGWPVSHSRSPRLHGFWLEQMGIDGAYLPLAVAPEHLETVIRALPRMGFA 62 Query: 65 GLNVTIPFKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAIQAPG 124 G NVT+P KE + + D LAR GA N LV +DG++ NTD G + P Sbjct: 63 GANVTVPHKEAVMRLVDHLDPLARRIGAVNTLVVRQDGTLEGRNTDAYGFFENLRQGCPL 122 Query: 125 FDVTAAPVVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAKGEDA 184 ++ T+ P ++GAGGAAR VAAL AG P I + NR+ RA LA G V Sbjct: 123 WEPTSGPAAVIGAGGAARAVVAALADAGVPEIRLANRSRERAATLAADLGGPVTVVDWAE 182 Query: 185 LPALLPEAGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEAAGRR 244 L L++N T+LG+ G + DL P T+VV D+VY PL T+ L RA A G Sbjct: 183 RAESLEGCALLVNTTTLGMTGQSSLDLDLAALPTTSVVNDIVYVPLVTDLLARATARGNP 242 Query: 245 TVDGLEMLLRQAIPTFETIYGQAPSPKIDVRVLAL 279 VDGL MLL QA+P FE +GQ P +R L Sbjct: 243 IVDGLGMLLHQAVPGFEAWFGQRPQVSDQLRAFVL 277 Lambda K H 0.319 0.136 0.390 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: 203 Number of extensions: 9 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: 285 Length of database: 278 Length adjustment: 26 Effective length of query: 259 Effective length of database: 252 Effective search space: 65268 Effective search space used: 65268 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_043745705.1 AMB_RS23010 (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.8405.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-69 218.5 0.0 5.5e-69 218.3 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_043745705.1 AMB_RS23010 shikimate dehydrogen Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_043745705.1 AMB_RS23010 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 218.3 0.0 5.5e-69 5.5e-69 2 260 .. 9 270 .. 8 276 .. 0.94 Alignments for each domain: == domain 1 score: 218.3 bits; conditional E-value: 5.5e-69 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 l gv+G p+ hS sp +h l+q+g+++ Yl + v +e+le ++ ++ g+ G+nvTvP+Ke+v++l lcl|NCBI__GCF_000009985.1:WP_043745705.1 9 LAGVLGWPVSHSRSPRLHGFWLEQMGIDGAYLPLAVAPEHLETVIRALPRMGFAGANVTVPHKEAVMRL 77 579****************************************************************** PP TIGR00507 71 lDeieesakligavNTlk.ledgklvgynTDgiGlvssLek...lsklksekrvliiGAGGaakavale 135 +D++++ a+ igavNTl+ ++dg l+g nTD++G++ +L++ l ++ +++iGAGGaa+av+ + lcl|NCBI__GCF_000009985.1:WP_043745705.1 78 VDHLDPLARRIGAVNTLVvRQDGTLEGRNTDAYGFFENLRQgcpLWEPT-SGPAAVIGAGGAARAVVAA 145 *****************988999******************74333333.56799************** PP TIGR00507 136 Llka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkael 203 L++a e+ +aNR+ e+a la l +++ + + l+ l++n+t +g++g+ ++ lcl|NCBI__GCF_000009985.1:WP_043745705.1 146 LADAgVPEIRLANRSRERAATLAADLGGPVTVVDWAERAESLEGCALLVNTTTLGMTGQS-SLDLDLAA 213 ****5569******************99999*****99*********************9.89999999 PP TIGR00507 204 lkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvek 260 l + ++v D+vy pl t ll+ a +g +++dGlgMl +Qa+ Fe w+g+ p+v+ lcl|NCBI__GCF_000009985.1:WP_043745705.1 214 LPTTSVVNDIVYVPLVTDLLARATARGNPIVDGLGMLLHQAVPGFEAWFGQRPQVSD 270 9****************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (278 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: 9.85 // [ok]
This GapMind analysis is from Apr 09 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