Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate AO353_10670 AO353_10670 shikimate dehydrogenase
Query= BRENDA::Q88RQ5 (274 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10670 Length = 273 Score = 437 bits (1123), Expect = e-127 Identities = 215/272 (79%), Positives = 244/272 (89%) Query: 1 MDQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGGNVT 60 MD+YVVFGNPIGHSKSPLIHRLFAEQT Q L+Y+TLLAPLD+FS CA FF++G G NVT Sbjct: 1 MDRYVVFGNPIGHSKSPLIHRLFAEQTAQKLDYSTLLAPLDDFSGCATEFFREGRGANVT 60 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120 VPFKEEA+RL +SLT RA+RAGAVNTLSKLADG+L GDNTDGAGLVRDLTVNAG L GK Sbjct: 61 VPFKEEAYRLANSLTERAQRAGAVNTLSKLADGSLLGDNTDGAGLVRDLTVNAGFSLRGK 120 Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQEP 180 RIL+LGAGGAVRG LEP+LA +P S++IANRT+EKAE LA F +LGPV ASGF WL+EP Sbjct: 121 RILLLGAGGAVRGALEPLLAEQPASVIIANRTLEKAELLAELFADLGPVSASGFDWLREP 180 Query: 181 VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGLG 240 VD+IINATSASL+G++PPIA SL+E G+TVCYDMMYGKEPT FC+WA++ GAA +DGLG Sbjct: 181 VDLIINATSASLSGDVPPIASSLIEPGKTVCYDMMYGKEPTSFCRWASEHGAAVSMDGLG 240 Query: 241 MLAEQAAEAFFIWRGVRPDTAPVLAELRRQLA 272 MLAEQAAEAFF+WRGVRPDTAPVLAELRRQLA Sbjct: 241 MLAEQAAEAFFLWRGVRPDTAPVLAELRRQLA 272 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: 328 Number of extensions: 11 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: 274 Length of database: 273 Length adjustment: 25 Effective length of query: 249 Effective length of database: 248 Effective search space: 61752 Effective search space used: 61752 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 AO353_10670 AO353_10670 (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.31887.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-79 251.0 0.0 6.6e-79 250.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_10670 AO353_10670 shikimate dehydrogen Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_10670 AO353_10670 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 250.8 0.0 6.6e-79 6.6e-79 3 269 .. 4 271 .. 2 272 .. 0.93 Alignments for each domain: == domain 1 score: 250.8 bits; conditional E-value: 6.6e-79 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeev 67 + v+Gnpi hSksplih +++q+ ++l Y + +++++++ ++++ +g +G+nvTvPfKee+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_10670 4 YVVFGNPIGHSKSPLIHRLFAEQTAQKLDYSTLLAPLDDFSGCATEFFREG-RGANVTVPFKEEA 67 78***********************************************99.8************ PP TIGR00507 68 lellDeieesakligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaak 130 ++l+ ++e+a+ +gavNTl l dg l+g+nTDg Glv +L + +kr+l++GAGGa + lcl|FitnessBrowser__pseudo3_N2E3:AO353_10670 68 YRLANSLTERAQRAGAVNTLSkLADGSLLGDNTDGAGLVRDLTVnAGFSLRGKRILLLGAGGAVR 132 ********************99********************997666556************** PP TIGR00507 131 avaleLlka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgei 194 +++ +Ll + + +viiaNRt+ekae lae ++ lg + a + + + vdliinatsa+lsg++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_10670 133 GALEPLLAEqPASVIIANRTLEKAELLAELFADLGPVSASGFDWL-REPVDLIINATSASLSGDV 196 ****98866489***********************9988775554.567**************** PP TIGR00507 195 deaevkaellkegk.lvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepd 257 +++ ++l++ gk +++D++y + t + ++a+++g + +dGlgMl +Qaa +F lw+gv pd lcl|FitnessBrowser__pseudo3_N2E3:AO353_10670 197 --PPIASSLIEPGKtVCYDMMYGKEPTSFCRWASEHGaAVSMDGLGMLAEQAAEAFFLWRGVRPD 259 ..********98863789*******************66678*********************** PP TIGR00507 258 vekvfealkekl 269 v l+++l lcl|FitnessBrowser__pseudo3_N2E3:AO353_10670 260 TAPVLAELRRQL 271 ***999998887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (273 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: 00:00:00.01 # Mc/sec: 6.96 // [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