Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate CCNA_00003 CCNA_00003 shikimate 5-dehydrogenase
Query= reanno::Caulo:CCNA_00003 (285 letters) >FitnessBrowser__Caulo:CCNA_00003 Length = 285 Score = 550 bits (1417), Expect = e-161 Identities = 285/285 (100%), Positives = 285/285 (100%) Query: 1 MTNAITGAAIVGGVCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRG 60 MTNAITGAAIVGGVCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRG Sbjct: 1 MTNAITGAAIVGGVCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRG 60 Query: 61 GAVRGLNVTIPFKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAI 120 GAVRGLNVTIPFKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAI Sbjct: 61 GAVRGLNVTIPFKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAI 120 Query: 121 QAPGFDVTAAPVVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAK 180 QAPGFDVTAAPVVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAK Sbjct: 121 QAPGFDVTAAPVVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAK 180 Query: 181 GEDALPALLPEAGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEA 240 GEDALPALLPEAGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEA Sbjct: 181 GEDALPALLPEAGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEA 240 Query: 241 AGRRTVDGLEMLLRQAIPTFETIYGQAPSPKIDVRVLALKLLGEV 285 AGRRTVDGLEMLLRQAIPTFETIYGQAPSPKIDVRVLALKLLGEV Sbjct: 241 AGRRTVDGLEMLLRQAIPTFETIYGQAPSPKIDVRVLALKLLGEV 285 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: 412 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: 285 Length adjustment: 26 Effective length of query: 259 Effective length of database: 259 Effective search space: 67081 Effective search space used: 67081 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 CCNA_00003 CCNA_00003 (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.698.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-64 204.3 0.0 1.2e-64 204.0 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_00003 CCNA_00003 shikimate 5-dehydroge Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_00003 CCNA_00003 shikimate 5-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 204.0 0.0 1.2e-64 1.2e-64 4 257 .. 13 269 .. 10 281 .. 0.90 Alignments for each domain: == domain 1 score: 204.0 bits; conditional E-value: 1.2e-64 TIGR00507 4 gviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeiee 76 gv G+pikhS+sp+ihna ++ gl+ Y+ f +++e +++g++ ++G+nvT+PfKe++l+++D ++ lcl|FitnessBrowser__Caulo:CCNA_00003 13 GVCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRGGAVRGLNVTIPFKERALAVADTASD 85 8************************************************************************ PP TIGR00507 77 sakligavNTlk.ledgklvgynTDgiGlvssLekls..klksekrvliiGAGGaakavaleLlka.dkevii 145 a+++ga N l+ edg + ++nTDg Gl+ ++ + + + v+i+GAGGaa++++ +Ll a ++ + lcl|FitnessBrowser__Caulo:CCNA_00003 86 LARMAGAANLLVfNEDGSVHADNTDGPGLLGAIAIQApgFDVTAAPVVILGAGGAARGAVAALLLAgAPRIAV 158 ************8899*************988876331133347899**********9888887774789*** PP TIGR00507 146 aNRtvekaeelaerlqelgeilalsleevelkk..vdliinatsaglsgeideaevkaellkegklvvDlvyn 216 +NRtv++a++la+++ e +++a ++ ++ liinats+gl g ++ + l + ++v+D+vy+ lcl|FitnessBrowser__Caulo:CCNA_00003 159 VNRTVARAQDLADTFGE--KVVAKGEDALPALLpeAGLIINATSLGLGGGA-GPSADLTLTPKTAVVMDMVYK 228 **************999..55555666666543349*************99.9999999************** PP TIGR00507 217 pletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepd 257 pl t +l+ a+ g +++dGl+Ml Qa Fe g+ p lcl|FitnessBrowser__Caulo:CCNA_00003 229 PLRTEFLRRAEAAGRRTVDGLEMLLRQAIPTFETIYGQAPS 269 *********************************99999864 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: 9.74 // [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