Align ketol-acid reductoisomerase (NAD+) (EC 1.1.1.382); ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_014450633.1 LFE_RS12750 ketol-acid reductoisomerase
Query= BRENDA::C8WR67 (344 letters) >NCBI__GCF_000284315.1:WP_014450633.1 Length = 339 Score = 447 bits (1150), Expect = e-130 Identities = 217/330 (65%), Positives = 262/330 (79%) Query: 2 EKIYYDADISIQPLADKRIAVIGYGSQGHAHAQNLRDSGFDVVIGLRPGSSWAKAEADGF 61 +KI Y++D++++ + K++A+IG+GSQGHAHA NLR+S V IGLRPG+SW KAE GF Sbjct: 3 KKISYESDLNLKLIQGKKVAIIGFGSQGHAHALNLRESAVSVEIGLRPGASWTKAEGFGF 62 Query: 62 RVMAVGEAVEESDVIMILLPDERQPAVYEREIRPYLTAGKALAFAHGFNIHFSQIQPPKD 121 + + V EAV+++D +MILLPDE Q +Y EIRP L G LAF HGFNIHF QI PPKD Sbjct: 63 KPVTVSEAVKKADFVMILLPDELQGDIYRDEIRPNLRPGMTLAFGHGFNIHFGQITPPKD 122 Query: 122 VDVFMVAPKGPGHLVRRVYEAGGGVPALIAVHQDASGQAKDLALAYARGIGAGRAGILTT 181 VDV ++APKGPGHLVR Y+ G GVPALIA+HQDA+ AKDLAL+YA IG GR GI T Sbjct: 123 VDVMLIAPKGPGHLVRSEYQKGSGVPALIAIHQDATKTAKDLALSYAGAIGGGRPGIFET 182 Query: 182 TFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPEIAYFECLHEMKLIVDLIYEG 241 TFREETETDLFGEQ VLCGGL+ALI AGFETL EAGY PE+AYFECLHE+KLIVDLIYEG Sbjct: 183 TFREETETDLFGEQVVLCGGLTALITAGFETLTEAGYAPEMAYFECLHEVKLIVDLIYEG 242 Query: 242 GLEYMRYSISDTAQWGDFTSGPRIINEETKKEMRRILADIQSGAFAKSWILENQANRPMF 301 G+ MRYSIS+TA++GD T GPRII ETK EM++IL +IQSG FAK +ILEN+A RP+F Sbjct: 243 GISNMRYSISNTAEYGDLTRGPRIITSETKAEMKKILHEIQSGQFAKEFILENKAGRPVF 302 Query: 302 NAINRRELEHPIEVVGRKLRSMMPFIKAKR 331 A+ + HPIE VG ++RSMMP+I R Sbjct: 303 QALEKSGQNHPIEKVGNEIRSMMPWIGKSR 332 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: 396 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: 344 Length of database: 339 Length adjustment: 29 Effective length of query: 315 Effective length of database: 310 Effective search space: 97650 Effective search space used: 97650 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 WP_014450633.1 LFE_RS12750 (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.885769.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-140 453.8 0.0 1.5e-140 453.6 0.0 1.0 1 NCBI__GCF_000284315.1:WP_014450633.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000284315.1:WP_014450633.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 453.6 0.0 1.5e-140 1.5e-140 1 312 [. 16 327 .. 16 329 .. 0.99 Alignments for each domain: == domain 1 score: 453.6 bits; conditional E-value: 1.5e-140 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 ++gkkvaiiG+GsqG+a+alnlr+s + v +glr++ asw+kAe Gfk +tv+ea+kkad++miLlpDe+q NCBI__GCF_000284315.1:WP_014450633.1 16 IQGKKVAIIGFGSQGHAHALNLRESAVSVEIGLRPG-ASWTKAEGFGFKPVTVSEAVKKADFVMILLPDELQG 87 689*******************************98.9*********************************** PP TIGR00465 74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146 + y+ ei+p+l+ g +l f HGfni+f qi++pkdvdv+l+APKgpG+lvR+ey++g Gvp+liA++qd+t NCBI__GCF_000284315.1:WP_014450633.1 88 DIYRDEIRPNLRPGMTLAFGHGFNIHFGQITPPKDVDVMLIAPKGPGHLVRSEYQKGSGVPALIAIHQDATKT 160 ************************************************************************* PP TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219 ak+ Al+yA aiGg+r g++ettF+eE+e+DLfGEq+vLcGgl+ali a+f+tL+eaGy+pe+Ayfe++he+k NCBI__GCF_000284315.1:WP_014450633.1 161 AKDLALSYAGAIGGGRPGIFETTFREETETDLFGEQVVLCGGLTALITAGFETLTEAGYAPEMAYFECLHEVK 233 ************************************************************************* PP TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291 livdl++e+G+++mr ++sntA++g+l+++ +i++ e+k+em+kil+eiq+G+fake++le++ag+p f++ + NCBI__GCF_000284315.1:WP_014450633.1 234 LIVDLIYEGGISNMRYSISNTAEYGDLTRGpRIITSETKAEMKKILHEIQSGQFAKEFILENKAGRPVFQALE 306 ************************************************************************* PP TIGR00465 292 kkekeqeiekvGkelralvka 312 k+ +++ iekvG+e+r ++++ NCBI__GCF_000284315.1:WP_014450633.1 307 KSGQNHPIEKVGNEIRSMMPW 327 *******************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (339 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: 23.44 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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