Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate WP_011423409.1 RHE_RS00020 shikimate dehydrogenase
Query= reanno::Caulo:CCNA_00003 (285 letters) >NCBI__GCF_000092045.1:WP_011423409.1 Length = 285 Score = 199 bits (505), Expect = 8e-56 Identities = 122/266 (45%), Positives = 151/266 (56%), Gaps = 4/266 (1%) Query: 14 VCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRGGAVR--GLNVTIP 71 V G PIKHS SP+IH W+ GL +Y A D F F+ L+ G+ G NVTIP Sbjct: 14 VTGFPIKHSRSPLIHGYWLKTLGLPGSYRAHEVAPDAFPDFIASLKDGSSDFIGGNVTIP 73 Query: 72 FKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAIQAPGFDVTAAP 131 KE A +AD DLA GA+N L + EDG +HA NTDG G + + PG+D Sbjct: 74 HKELAFRLADKPDDLAHELGASNTL-WLEDGLLHATNTDGRGFTANLDERHPGWD-RHDT 131 Query: 132 VVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAKGEDALPALLPE 191 V+ GAGGA+R + A+ G I VVNRTV RA++LAD FG KV A AL ++ Sbjct: 132 AVVFGAGGASRAIIQAVRDRGFREIHVVNRTVERARELADRFGPKVRAHPVGALAEVMHG 191 Query: 192 AGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEAAGRRTVDGLEM 251 AGL +N TSLG+ G A P D AVV D+VY PL T LR+AE G VDGL M Sbjct: 192 AGLFVNTTSLGMDGEAAPLIDFAPLAADAVVTDIVYIPLNTPILRQAEEQGLSVVDGLGM 251 Query: 252 LLRQAIPTFETIYGQAPSPKIDVRVL 277 LL QA+P FE +G+ P +R L Sbjct: 252 LLHQAVPGFEKWFGERPVVDAALRAL 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: 235 Number of extensions: 18 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: 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 WP_011423409.1 RHE_RS00020 (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.5526.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-67 211.8 0.0 6.7e-67 211.4 0.0 1.0 1 lcl|NCBI__GCF_000092045.1:WP_011423409.1 RHE_RS00020 shikimate dehydrogen Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092045.1:WP_011423409.1 RHE_RS00020 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 211.4 0.0 6.7e-67 6.7e-67 5 264 .. 14 276 .. 11 280 .. 0.93 Alignments for each domain: == domain 1 score: 211.4 bits; conditional E-value: 6.7e-67 TIGR00507 5 viGnpikhSksplihnaalkqlgleleYlafeveieelekalsgika..lglkGvnvTvPfKeevlell 71 v G pikhS splih lk+lgl + Y a+ev ++++++++ +k + G nvT+P+Ke +++l+ lcl|NCBI__GCF_000092045.1:WP_011423409.1 14 VTGFPIKHSRSPLIHGYWLKTLGLPGSYRAHEVAPDAFPDFIASLKDgsSDFIGGNVTIPHKELAFRLA 82 789*****************************************996226799**************** PP TIGR00507 72 DeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka 139 D+ ++ a+++ga NTl ledg l + nTDg G++++L + + ++++ GAGGa++a++ + + lcl|NCBI__GCF_000092045.1:WP_011423409.1 83 DKPDDLAHELGASNTLWLEDGLLHATNTDGRGFTANLDErHPGWDRHDTAVVFGAGGASRAIIQAVRDR 151 *************************************996555566899******************99 PP TIGR00507 140 .dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkeg 207 e+ ++NRtve+a+ela+r+ + + l +n+ts+g+ ge + ++ l+++ lcl|NCBI__GCF_000092045.1:WP_011423409.1 152 gFREIHVVNRTVERARELADRFGPKVRAHPVGALAEVMHGAGLFVNTTSLGMDGEA-APLIDFAPLAAD 219 5589********************8888888888888999***************9.899********* PP TIGR00507 208 klvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfea 264 ++v D+vy+pl+tp+l+ a+++g +v+dGlgMl +Qa+ Fe+w+g p v+ + +a lcl|NCBI__GCF_000092045.1:WP_011423409.1 220 AVVTDIVYIPLNTPILRQAEEQGLSVVDGLGMLLHQAVPGFEKWFGERPVVDAALRA 276 ***********************************************9988877665 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.90 // [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