Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate SMc02791 SMc02791 shikimate 5-dehydrogenase
Query= reanno::Caulo:CCNA_00003 (285 letters) >FitnessBrowser__Smeli:SMc02791 Length = 286 Score = 191 bits (485), Expect = 2e-53 Identities = 114/257 (44%), Positives = 150/257 (58%), Gaps = 4/257 (1%) Query: 14 VCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRGGAVR--GLNVTIP 71 V G P+KHS SP+IH W+ G+ +Y + F F+ ++ G G NVTIP Sbjct: 14 VTGYPVKHSRSPLIHGHWLKQFGIRGSYRAHEVTPEAFPDFMRQIKEGRTDFCGGNVTIP 73 Query: 72 FKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAIQAPGFDVTAAP 131 KE A +AD +L+ GAAN L + E+G + A NTDG G + + +A G+D +A Sbjct: 74 HKEAAFRLADRPDELSAELGAANTL-WLENGKIRATNTDGRGFVANLDERAKGWDRISA- 131 Query: 132 VVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAKGEDALPALLPE 191 VILGAGGA+R + A+ G I VVNRT RA++LAD FG V A ALP ++ Sbjct: 132 AVILGAGGASRAVIQAIRDRGVKTIHVVNRTPERARELADRFGTAVHAHSMAALPEVVSG 191 Query: 192 AGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEAAGRRTVDGLEM 251 AGL +N TSLG+ G P+ D + AVV D+VY PL+T LR+AE G R VDGL M Sbjct: 192 AGLFVNTTSLGMDGEPAPAIDFSGLAPDAVVTDIVYVPLKTPLLRQAEEQGFRIVDGLGM 251 Query: 252 LLRQAIPTFETIYGQAP 268 LL QA+P FE +G P Sbjct: 252 LLHQAVPGFEKWFGLRP 268 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: 216 Number of extensions: 14 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: 285 Length of database: 286 Length adjustment: 26 Effective length of query: 259 Effective length of database: 260 Effective search space: 67340 Effective search space used: 67340 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 SMc02791 SMc02791 (shikimate 5-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.29709.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-72 227.4 0.0 1.2e-71 227.0 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMc02791 SMc02791 shikimate 5-dehydrogena Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc02791 SMc02791 shikimate 5-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 227.0 0.0 1.2e-71 1.2e-71 5 265 .. 14 277 .. 11 282 .. 0.92 Alignments for each domain: == domain 1 score: 227.0 bits; conditional E-value: 1.2e-71 TIGR00507 5 viGnpikhSksplihnaalkqlgleleYlafeveieelekalsgika..lglkGvnvTvPfKeevlellDeiees 77 v G+p+khS splih + lkq+g+ + Y a+ev++e++++++ +ik+ + G nvT+P+Ke++++l+D+ +e lcl|FitnessBrowser__Smeli:SMc02791 14 VTGYPVKHSRSPLIHGHWLKQFGIRGSYRAHEVTPEAFPDFMRQIKEgrTDFCGGNVTIPHKEAAFRLADRPDEL 88 78*******************************************97436799********************** PP TIGR00507 78 akligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka.dkeviiaNRtv 150 +++ga NTl le+gk+ + nTDg G+v++L + + ++i+GAGGa++av+ ++ + k++ ++NRt lcl|FitnessBrowser__Smeli:SMc02791 89 SAELGAANTLWLENGKIRATNTDGRGFVANLDErAKGWDRISAAVILGAGGASRAVIQAIRDRgVKTIHVVNRTP 163 *******************************9976666668899*****************9956899******* PP TIGR00507 151 ekaeelaerlqelgeilalsleevelkk..vdliinatsaglsgeideaevkaellkegklvvDlvynpletpll 223 e+a+ela+r+ + + a s++ +++ l +n+ts+g+ ge ++++ + l+ +++v D+vy pl+tpll lcl|FitnessBrowser__Smeli:SMc02791 164 ERARELADRFGT--AVHAHSMAALPEVVsgAGLFVNTTSLGMDGEP-APAIDFSGLAPDAVVTDIVYVPLKTPLL 235 ***********9..55566666666543349*************98.9*************************** PP TIGR00507 224 keakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfeal 265 + a+++g +++dGlgMl +Qa+ Fe+w+g p v+++ +++ lcl|FitnessBrowser__Smeli:SMc02791 236 RQAEEQGFRIVDGLGMLLHQAVPGFEKWFGLRPVVDETLRQI 277 *********************************999887765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (286 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: 7.95 // [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