Align ketol-acid reductoisomerase (NAD+) (EC 1.1.1.382); ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate Synpcc7942_1552 Synpcc7942_1552 ketol-acid reductoisomerase
Query= BRENDA::C8WR67 (344 letters) >FitnessBrowser__SynE:Synpcc7942_1552 Length = 327 Score = 449 bits (1155), Expect = e-131 Identities = 225/326 (69%), Positives = 266/326 (81%), Gaps = 1/326 (0%) Query: 4 IYYDADISIQPLADKRIAVIGYGSQGHAHAQNLRDSGFDVVIGLRPGS-SWAKAEADGFR 62 +YYDAD ++ L K +A+IGYGSQGHAHA NLRDSG +VV+GL PGS S AKAEA+G + Sbjct: 1 MYYDADANLDLLNGKTVAIIGYGSQGHAHALNLRDSGVNVVVGLYPGSKSAAKAEAEGLK 60 Query: 63 VMAVGEAVEESDVIMILLPDERQPAVYEREIRPYLTAGKALAFAHGFNIHFSQIQPPKDV 122 V+ V EA + +D IMILLPDE Q +V+E EIRP L+AGK LAFAHGFNIHF+QI PP DV Sbjct: 61 VLPVAEAAQAADWIMILLPDEFQKSVFENEIRPALSAGKVLAFAHGFNIHFAQIVPPADV 120 Query: 123 DVFMVAPKGPGHLVRRVYEAGGGVPALIAVHQDASGQAKDLALAYARGIGAGRAGILTTT 182 DV M+APK PGHLVRR YE G GVP L A++QDASGQA+D A+AYA+GIG RAGIL T+ Sbjct: 121 DVVMIAPKSPGHLVRRTYEQGQGVPCLFAIYQDASGQARDRAMAYAKGIGGTRAGILETS 180 Query: 183 FREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPEIAYFECLHEMKLIVDLIYEGG 242 FREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPE+AYFECLHE+KLIVDLI EGG Sbjct: 181 FREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPELAYFECLHEVKLIVDLIVEGG 240 Query: 243 LEYMRYSISDTAQWGDFTSGPRIINEETKKEMRRILADIQSGAFAKSWILENQANRPMFN 302 L MR SIS+TA++GD+ +GPR+I EETK EM+R+LADIQ G FA ++ E A +P+ Sbjct: 241 LAAMRDSISNTAEYGDYVTGPRLITEETKAEMKRVLADIQQGRFALDFVQECGAGKPVMT 300 Query: 303 AINRRELEHPIEVVGRKLRSMMPFIK 328 A R E EHPIE VG+ LR+M ++K Sbjct: 301 ATRRLEAEHPIESVGKDLRAMFSWLK 326 Lambda K H 0.320 0.138 0.404 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: 388 Number of extensions: 13 Number of successful extensions: 2 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: 344 Length of database: 327 Length adjustment: 28 Effective length of query: 316 Effective length of database: 299 Effective search space: 94484 Effective search space used: 94484 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: 49 (23.5 bits)
Align candidate Synpcc7942_1552 Synpcc7942_1552 (ketol-acid reductoisomerase)
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))
# 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/TIGR00465.hmm # target sequence database: /tmp/gapView.3324.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00465 [M=314] Accession: TIGR00465 Description: ilvC: ketol-acid reductoisomerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-147 474.4 0.0 7.9e-147 474.2 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1552 Synpcc7942_1552 ketol-acid reduc Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1552 Synpcc7942_1552 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 474.2 0.0 7.9e-147 7.9e-147 1 313 [. 12 325 .. 12 326 .. 0.99 Alignments for each domain: == domain 1 score: 474.2 bits; conditional E-value: 7.9e-147 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 l+gk+vaiiGyGsqG+a+alnlrdsg+nv+vgl+++++s +kAe +G+kvl v+ea+++ad imiLlpD lcl|FitnessBrowser__SynE:Synpcc7942_1552 12 LNGKTVAIIGYGSQGHAHALNLRDSGVNVVVGLYPGSKSAAKAEAEGLKVLPVAEAAQAADWIMILLPD 80 689****************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e qk+v+e+ei+p l +gk+l f+HGfni+f+qiv+p+dvdvv++APK+pG+lvR++y++g+Gvp l+A lcl|FitnessBrowser__SynE:Synpcc7942_1552 81 EFQKSVFENEIRPALSAGKVLAFAHGFNIHFAQIVPPADVDVVMIAPKSPGHLVRRTYEQGQGVPCLFA 149 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 ++qd++g+a++ A+ayAk+iGg+rag+let+F+eE+e+DLfGEqavLcGgl+alika+f+tLveaGyqp lcl|FitnessBrowser__SynE:Synpcc7942_1552 150 IYQDASGQARDRAMAYAKGIGGTRAGILETSFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQP 218 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 elAyfe++he+klivdl+ e+Gl+ mrd++sntA++g++ ++ + ++ee+k+em+ +l +iq+G+fa + lcl|FitnessBrowser__SynE:Synpcc7942_1552 219 ELAYFECLHEVKLIVDLIVEGGLAAMRDSISNTAEYGDYVTGpRLITEETKAEMKRVLADIQQGRFALD 287 ******************************************9************************** PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkae 313 ++ e agkp ++++r+ e e+ ie+vGk+lra++++ lcl|FitnessBrowser__SynE:Synpcc7942_1552 288 FVQECGAGKPVMTATRRLEAEHPIESVGKDLRAMFSWL 325 ***********************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (327 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: 11.07 // [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