Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_008807976.1 KVAR_RS24825 ketol-acid reductoisomerase
Query= BRENDA::A6TGG1 (491 letters) >NCBI__GCF_000025465.1:WP_008807976.1 Length = 491 Score = 966 bits (2497), Expect = 0.0 Identities = 488/491 (99%), Positives = 488/491 (99%) Query: 1 MANYFNTLNLRQQLAQLGKCRFMARDEFADGASYLQGKKVVIVGCGAQGLNQGLNMRDSG 60 MANYFNTLNLRQQLAQLGKCRFM RDEFADGASYLQGKKVVIVGCGAQGLNQGLNMRDSG Sbjct: 1 MANYFNTLNLRQQLAQLGKCRFMGRDEFADGASYLQGKKVVIVGCGAQGLNQGLNMRDSG 60 Query: 61 LDISYALRKEAIAEKRASWRKATENGFKVGTYEELIPQADLVVNLTPDKQHSDVVRSVQP 120 LDISYALRKEAIAEKRASWRKATENGFKVGTYEELIPQADLVVNLTPDKQHSDVVRSVQP Sbjct: 61 LDISYALRKEAIAEKRASWRKATENGFKVGTYEELIPQADLVVNLTPDKQHSDVVRSVQP 120 Query: 121 LMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180 LMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE Sbjct: 121 LMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180 Query: 181 NDPKGEGMAIAKAWAAATGGHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKL 240 NDPKGEGMAIAKAWAAATGGHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKL Sbjct: 181 NDPKGEGMAIAKAWAAATGGHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKL 240 Query: 241 VAEGTDPAYAEKLIQFGWETITEALKQGGITLMMDRLSNPAKLRAYALSEQLKEIMAPLF 300 VAEGTDPAYAEKLIQFGWETITEALKQGGITLMMDRLSNPAKLRAYALSEQLKEIMAPLF Sbjct: 241 VAEGTDPAYAEKLIQFGWETITEALKQGGITLMMDRLSNPAKLRAYALSEQLKEIMAPLF 300 Query: 301 QKHMDDIISGEFSSGMMADWANDDKKLLTWREETGKTAFETAPQYEGKIGEQEYFDKGVL 360 QKHMDDIISGEFSSGMMADWANDDKKLLTWREETGKTAFETAPQYEGKIGEQEYFDKGVL Sbjct: 301 QKHMDDIISGEFSSGMMADWANDDKKLLTWREETGKTAFETAPQYEGKIGEQEYFDKGVL 360 Query: 361 MIAMVKAGVELAFETMVASGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYG 420 MIAMVKAGVELAFETMV SGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYG Sbjct: 361 MIAMVKAGVELAFETMVDSGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYG 420 Query: 421 NYLFSYACVPLLKEFMTTLQTGDLGTAIAEGAVDNAQLRDVNEAIRSHAIEQVGKKLRGY 480 NYLFSYACVPLLKEFMTTLQTGDLG AIAEGAVDNAQLRDVNEAIRSHAIEQVGKKLRGY Sbjct: 421 NYLFSYACVPLLKEFMTTLQTGDLGKAIAEGAVDNAQLRDVNEAIRSHAIEQVGKKLRGY 480 Query: 481 MTDMKRIAVAG 491 MTDMKRIAVAG Sbjct: 481 MTDMKRIAVAG 491 Lambda K H 0.317 0.134 0.384 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: 944 Number of extensions: 24 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: 491 Length of database: 491 Length adjustment: 34 Effective length of query: 457 Effective length of database: 457 Effective search space: 208849 Effective search space used: 208849 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
Align candidate WP_008807976.1 KVAR_RS24825 (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.13403.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-155 503.0 1.1 7.3e-141 454.6 0.2 2.0 2 lcl|NCBI__GCF_000025465.1:WP_008807976.1 KVAR_RS24825 ketol-acid reductoi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025465.1:WP_008807976.1 KVAR_RS24825 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 454.6 0.2 7.3e-141 7.3e-141 1 313 [. 35 368 .. 35 369 .. 0.98 2 ! 51.5 0.1 3.9e-18 3.9e-18 188 311 .. 364 482 .. 364 485 .. 0.93 Alignments for each domain: == domain 1 score: 454.6 bits; conditional E-value: 7.3e-141 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea.....aswkkAeedGfkvltveeaikkadlim 64 l+gkkv+i+G+G+qG +q+ln+rdsgl+++++lrkea asw+kA+e+Gfkv t+ee+i++adl++ lcl|NCBI__GCF_000025465.1:WP_008807976.1 35 LQGKKVVIVGCGAQGLNQGLNMRDSGLDISYALRKEAiaekrASWRKATENGFKVGTYEELIPQADLVV 103 79******************************************************************* PP TIGR00465 65 iLlpDevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGv 133 +L+pD+ q+++++++++pl+k+g+al++sHGfniv+++++i+kd++vv+vAPK+pG++vReeyk+g+Gv lcl|NCBI__GCF_000025465.1:WP_008807976.1 104 NLTPDK-QHSDVVRSVQPLMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGV 171 ******.99999999****************************************************** PP TIGR00465 134 psliAveqd..vtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtL 200 p+liAv+++ ++ge+++iA+a+A+a+Gg+ragvle++F++Ev+sDL+GEq++LcG+l+a+++++fd+L lcl|NCBI__GCF_000025465.1:WP_008807976.1 172 PTLIAVHPEndPKGEGMAIAKAWAAATGGHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKL 240 ******98877********************************************************** PP TIGR00465 201 veaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqn 269 v++G++p++A+++i++++++i+++lk++G++lm+d++sn+Akl+a++l+e+lke +++ +qk++++i++ lcl|NCBI__GCF_000025465.1:WP_008807976.1 241 VAEGTDPAYAEKLIQFGWETITEALKQGGITLMMDRLSNPAKLRAYALSEQLKEIMAPLFQKHMDDIIS 309 ********************************************************************* PP TIGR00465 270 Gefak....ewalek........eagkpafeearkke...keqeiekvGkelralvkae 313 Gef++ +wa+++ e+gk+afe+a+++e eqe++++G+ ++a+vka+ lcl|NCBI__GCF_000025465.1:WP_008807976.1 310 GEFSSgmmaDWANDDkklltwreETGKTAFETAPQYEgkiGEQEYFDKGVLMIAMVKAG 368 ****99999*****9**********************9999***************975 PP == domain 2 score: 51.5 bits; conditional E-value: 3.9e-18 TIGR00465 188 glealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelreilkeel 256 +++a++++af+t+v+ G +e Ay e +hel li++ + +k l +m +s+tA++g++ ++ + lcl|NCBI__GCF_000025465.1:WP_008807976.1 364 MVKAGVELAFETMVDSGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYGNYL----FSYAC 428 7999*****************************************************985....66778 PP TIGR00465 257 kkemqkilkeiqnGefakewalekeagkpafeearkkekeqeiekvGkelralvk 311 + +++ + +q+G+ k + e +++++++++ +++ + + ie+vGk+lr + lcl|NCBI__GCF_000025465.1:WP_008807976.1 429 VPLLKEFMTTLQTGDLGK-AIAEGAVDNAQLRDVNEAIRSHAIEQVGKKLRGYMT 482 89999999**********.777888**************************8765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (491 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 3.77 // [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