Align Ketol-acid reductoisomerase (NAD(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.382 (characterized)
to candidate 8499378 DvMF_0155 ketol-acid reductoisomerase (RefSeq)
Query= SwissProt::K4LVZ1 (332 letters) >FitnessBrowser__Miya:8499378 Length = 330 Score = 463 bits (1192), Expect = e-135 Identities = 222/330 (67%), Positives = 269/330 (81%) Query: 1 MKIYYDQDADLQYLDGKTVAVIGYGSQGHAQSQNLRDSGVKVVVADIPSSENWKKAEEAQ 60 MK+YY+QDA L+ L KTVA+IGYGSQGHA +QNLRDSG+ VVV P N++ A+E Sbjct: 1 MKVYYEQDATLEVLKDKTVAIIGYGSQGHAHAQNLRDSGINVVVGQRPGGANYELAKEHG 60 Query: 61 FQPLTADEAAREADIIQILVPDEKQAALYRESIAPNLRPGKALVFSHGFNIHFKQIVPPP 120 F PL EAA +AD+I IL+PD+ QAA+Y I PNL+PG AL+F+HGFNIHF QI PP Sbjct: 61 FAPLPVAEAAAKADLIMILLPDQVQAAIYEAEIKPNLKPGDALLFAHGFNIHFGQIEPPK 120 Query: 121 DVDVFMVAPKGPGHLVRRMYEEGAGVPSLVAVEQDYSGQALNLALAYAKGIGATRAGVIQ 180 DVDVFM+APKGPGHLVRR Y EG GVP LVA+ QD +G+A+ ALAYAKG+G R+GVI+ Sbjct: 121 DVDVFMIAPKGPGHLVRRTYTEGGGVPCLVAIHQDATGKAMEKALAYAKGVGGARSGVIE 180 Query: 181 TTFKEETETDLFGEQAVLCGGITELIRAGFDTLVDAGYQPEIAYFECLHEMKLIVDLIYE 240 TTFKEETETDLFGEQAVLCGG++ LI+AGF+TLV+AGYQPEIAYFECLHE+KLIVDLIYE Sbjct: 181 TTFKEETETDLFGEQAVLCGGLSSLIKAGFETLVEAGYQPEIAYFECLHEVKLIVDLIYE 240 Query: 241 GGISTMRYSISDTAEYGDLTRGKRIITEATREEMKKILKEIQDGVFAREWLLENQVGRPV 300 GG++ MR+SISDTAEYGD G+RI+ E T++EMKK+L+EIQ+G FAR ++LE + G P Sbjct: 241 GGLAKMRHSISDTAEYGDYVTGRRIVNEETKKEMKKVLQEIQEGTFARNFILEAKAGYPG 300 Query: 301 YNALRRKEQNHLIETVGARLRGMMPWLKKK 330 + A RR E +H IE VG +LRGMMPWL KK Sbjct: 301 FKATRRIEADHQIEQVGGKLRGMMPWLHKK 330 Lambda K H 0.318 0.136 0.393 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: 378 Number of extensions: 12 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: 332 Length of database: 330 Length adjustment: 28 Effective length of query: 304 Effective length of database: 302 Effective search space: 91808 Effective search space used: 91808 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: 49 (23.5 bits)
Align candidate 8499378 DvMF_0155 (ketol-acid reductoisomerase (RefSeq))
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.7136.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-146 471.2 0.2 7.9e-146 470.9 0.2 1.0 1 lcl|FitnessBrowser__Miya:8499378 DvMF_0155 ketol-acid reductoisom Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8499378 DvMF_0155 ketol-acid reductoisomerase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 470.9 0.2 7.9e-146 7.9e-146 1 312 [. 14 326 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 470.9 bits; conditional E-value: 7.9e-146 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqkevye 77 lk+k+vaiiGyGsqG+a+a nlrdsg+nv+vg r+++a ++ A+e Gf l v+ea++kadlimiLlpD+vq + ye lcl|FitnessBrowser__Miya:8499378 14 LKDKTVAIIGYGSQGHAHAQNLRDSGINVVVGQRPGGANYELAKEHGFAPLPVAEAAAKADLIMILLPDQVQAAIYE 90 79*************************************************************************** PP TIGR00465 78 aeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtgeakeiAlay 154 aeikp+lk g+allf+HGfni+f qi++pkdvdv+++APKgpG+lvR++y eg Gvp l+A++qd+tg+a+e+Alay lcl|FitnessBrowser__Miya:8499378 91 AEIKPNLKPGDALLFAHGFNIHFGQIEPPKDVDVFMIAPKGPGHLVRRTYTEGGGVPCLVAIHQDATGKAMEKALAY 167 ***************************************************************************** PP TIGR00465 155 AkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGle 231 Ak++Ggar gv+ettFkeE+e+DLfGEqavLcGgl+ lika+f+tLveaGyqpe+Ayfe++he+klivdl++e+Gl+ lcl|FitnessBrowser__Miya:8499378 168 AKGVGGARSGVIETTFKEETETDLFGEQAVLCGGLSSLIKAGFETLVEAGYQPEIAYFECLHEVKLIVDLIYEGGLA 244 ***************************************************************************** PP TIGR00465 232 lmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeearkkekeqeiekvGkelr 307 +mr+++s+tA++g++ ++ +i++ee+kkem+k+l+eiq+G+fa++++le +ag+p f+++r+ e +++ie+vG +lr lcl|FitnessBrowser__Miya:8499378 245 KMRHSISDTAEYGDYVTGrRIVNEETKKEMKKVLQEIQEGTFARNFILEAKAGYPGFKATRRIEADHQIEQVGGKLR 321 ***************9998********************************************************** PP TIGR00465 308 alvka 312 ++++ lcl|FitnessBrowser__Miya:8499378 322 GMMPW 326 ***98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (330 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: 9.75 // [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