Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_013981198.1 PST_RS00140 shikimate dehydrogenase
Query= BRENDA::Q88RQ5 (274 letters) >NCBI__GCF_000013785.1:WP_013981198.1 Length = 270 Score = 398 bits (1023), Expect = e-116 Identities = 202/271 (74%), Positives = 225/271 (83%), Gaps = 2/271 (0%) Query: 1 MDQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGGNVT 60 MD+Y VFGNPIGHSKSP IH LFA QTGQ L Y LLAPLD+F AR FF++G G NVT Sbjct: 1 MDRYGVFGNPIGHSKSPQIHALFAAQTGQALSYEPLLAPLDDFPAFARDFFREGRGANVT 60 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120 VPFKE+A+R+ D LT RARRAGAVNTL KL DG L GDNTDGAGLV DL +NAGV L+G+ Sbjct: 61 VPFKEQAYRMADELTERARRAGAVNTLKKLEDGRLLGDNTDGAGLVADL-LNAGVTLSGR 119 Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQEP 180 RIL+LGAGGAVRGVLEP+LAH+P +LVIANRT +AEQL +EF ELGP+ ASGFA L EP Sbjct: 120 RILLLGAGGAVRGVLEPLLAHRPAALVIANRTASRAEQLVQEFAELGPLSASGFAELAEP 179 Query: 181 VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGLG 240 VD+I+N TSASL GELPP+ADSL+ AGRT CYDMMY EPTPFC+WA LGA DGLG Sbjct: 180 VDLIVNGTSASLGGELPPLADSLIVAGRTFCYDMMYSAEPTPFCRWAAALGAT-TRDGLG 238 Query: 241 MLAEQAAEAFFIWRGVRPDTAPVLAELRRQL 271 ML EQAAEAF +WRGVRPDTAPVLAELRRQL Sbjct: 239 MLVEQAAEAFELWRGVRPDTAPVLAELRRQL 269 Lambda K H 0.319 0.137 0.405 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: 310 Number of extensions: 9 Number of successful extensions: 3 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: 274 Length of database: 270 Length adjustment: 25 Effective length of query: 249 Effective length of database: 245 Effective search space: 61005 Effective search space used: 61005 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_013981198.1 PST_RS00140 (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.21723.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-82 263.3 0.0 1.1e-82 263.2 0.0 1.0 1 lcl|NCBI__GCF_000013785.1:WP_013981198.1 PST_RS00140 shikimate dehydrogen Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013785.1:WP_013981198.1 PST_RS00140 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 263.2 0.0 1.1e-82 1.1e-82 3 269 .. 4 269 .. 2 270 .] 0.94 Alignments for each domain: == domain 1 score: 263.2 bits; conditional E-value: 1.1e-82 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlell 71 +gv+Gnpi hSksp ih +++q+g++l Y + +++++++ + ++ +g +G+nvTvPfKe++++++ lcl|NCBI__GCF_000013785.1:WP_013981198.1 4 YGVFGNPIGHSKSPQIHALFAAQTGQALSYEPLLAPLDDFPAFARDFFREG-RGANVTVPFKEQAYRMA 71 9************************************************99.8**************** PP TIGR00507 72 DeieesakligavNTlk.ledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka 139 De++e+a+ +gavNTlk ledg+l+g+nTDg Glv++L + s++r+l++GAGGa ++v+ +Ll + lcl|NCBI__GCF_000013785.1:WP_013981198.1 72 DELTERARRAGAVNTLKkLEDGRLLGDNTDGAGLVADLLNAGVTLSGRRILLLGAGGAVRGVLEPLLAH 140 *****************9**********************777777*******************9987 PP TIGR00507 140 .dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkeg 207 + +++iaNRt ++ae+l+++++elg a +e+ + vdli+n tsa+l ge+ +++ +l+ +g lcl|NCBI__GCF_000013785.1:WP_013981198.1 141 rPAALVIANRTASRAEQLVQEFAELGPLSASGFAELA-EPVDLIVNGTSASLGGEL--PPLADSLIVAG 206 799***********************99998877764.56****************..88888777665 PP TIGR00507 208 .klvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 ++++D++y tp+ ++a +g+ + dGlgMlv+Qaa +Felw+gv pd v l+++l lcl|NCBI__GCF_000013785.1:WP_013981198.1 207 rTFCYDMMYSAEPTPFCRWAAALGATTRDGLGMLVEQAAEAFELWRGVRPDTAPVLAELRRQL 269 16899************************************************9999988876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (270 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: 00:00:00.01 # Mc/sec: 7.12 // [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