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 WP_012101468.1 CKL_RS05360 ketol-acid reductoisomerase
Query= SwissProt::K4LVZ1 (332 letters) >NCBI__GCF_000016505.1:WP_012101468.1 Length = 333 Score = 458 bits (1179), Expect = e-134 Identities = 220/330 (66%), Positives = 266/330 (80%) Query: 1 MKIYYDQDADLQYLDGKTVAVIGYGSQGHAQSQNLRDSGVKVVVADIPSSENWKKAEEAQ 60 +KIYYD+D +L L KTVAV+GYGSQGHA +QNL+DSG+ VV+ S++WK+AEE Sbjct: 4 LKIYYDEDGNLDLLRDKTVAVLGYGSQGHAHAQNLKDSGINVVIGLYKGSKSWKRAEENG 63 Query: 61 FQPLTADEAAREADIIQILVPDEKQAALYRESIAPNLRPGKALVFSHGFNIHFKQIVPPP 120 F+ + A +A ++AD++ L+PDEKQ LY +SI NL GK L+F+HGFNIHF QI PP Sbjct: 64 FEVMEAADAVKKADMVMTLIPDEKQKGLYIDSIKDNLTEGKVLMFAHGFNIHFNQITPPE 123 Query: 121 DVDVFMVAPKGPGHLVRRMYEEGAGVPSLVAVEQDYSGQALNLALAYAKGIGATRAGVIQ 180 +VDV MVAPKGPGH+VRR Y EG GVP L AV QDYSG+A + ALAYAKGIG TR GV++ Sbjct: 124 NVDVIMVAPKGPGHIVRREYTEGKGVPCLYAVYQDYSGKAKDYALAYAKGIGGTRGGVLE 183 Query: 181 TTFKEETETDLFGEQAVLCGGITELIRAGFDTLVDAGYQPEIAYFECLHEMKLIVDLIYE 240 TTFK+ETETDLFGEQ VLCGGI+ELI+AGF+TLV+AGY PE AYFEC+HEMKLIVDL+ E Sbjct: 184 TTFKDETETDLFGEQVVLCGGISELIKAGFETLVEAGYAPENAYFECMHEMKLIVDLMNE 243 Query: 241 GGISTMRYSISDTAEYGDLTRGKRIITEATREEMKKILKEIQDGVFAREWLLENQVGRPV 300 GG+S MRYSISDTAEYGD + GKRI+TE TR+EMKK+L EIQDG FA+ W+LENQ GRP Sbjct: 244 GGLSYMRYSISDTAEYGDYSIGKRIVTEDTRKEMKKVLGEIQDGTFAKNWILENQTGRPS 303 Query: 301 YNALRRKEQNHLIETVGARLRGMMPWLKKK 330 + A R+KEQNH IE VG +LR MM W+ K Sbjct: 304 FIAKRKKEQNHPIEVVGKKLRAMMSWINSK 333 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: 388 Number of extensions: 9 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: 333 Length adjustment: 28 Effective length of query: 304 Effective length of database: 305 Effective search space: 92720 Effective search space used: 92720 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 WP_012101468.1 CKL_RS05360 (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.26036.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-150 485.2 1.2 4e-150 485.0 1.2 1.0 1 lcl|NCBI__GCF_000016505.1:WP_012101468.1 CKL_RS05360 ketol-acid reductois Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016505.1:WP_012101468.1 CKL_RS05360 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 485.0 1.2 4e-150 4e-150 1 312 [. 17 329 .. 17 331 .. 0.99 Alignments for each domain: == domain 1 score: 485.0 bits; conditional E-value: 4e-150 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 l++k+va++GyGsqG+a+a nl+dsg+nv++gl+k+++swk+Aee+Gf+v++ ++a+kkad++m+L+pD lcl|NCBI__GCF_000016505.1:WP_012101468.1 17 LRDKTVAVLGYGSQGHAHAQNLKDSGINVVIGLYKGSKSWKRAEENGFEVMEAADAVKKADMVMTLIPD 85 689****************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e qk y +ik++l+egk+l+f+HGfni+f+qi++p++vdv++vAPKgpG+ vR+ey eg+Gvp l+A lcl|NCBI__GCF_000016505.1:WP_012101468.1 86 EKQKGLYIDSIKDNLTEGKVLMFAHGFNIHFNQITPPENVDVIMVAPKGPGHIVRREYTEGKGVPCLYA 154 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+qd++g+ak++AlayAk+iGg+r gvlettFk+E+e+DLfGEq+vLcGg+++lika+f+tLveaGy+p lcl|NCBI__GCF_000016505.1:WP_012101468.1 155 VYQDYSGKAKDYALAYAKGIGGTRGGVLETTFKDETETDLFGEQVVLCGGISELIKAGFETLVEAGYAP 223 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e Ayfe++he+klivdl++e+Gl++mr ++s+tA++g+++ + +i++e ++kem+k+l eiq+G+fak+ lcl|NCBI__GCF_000016505.1:WP_012101468.1 224 ENAYFECMHEMKLIVDLMNEGGLSYMRYSISDTAEYGDYSIGkRIVTEDTRKEMKKVLGEIQDGTFAKN 292 *****************************************99************************** PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312 w+le+++g+p+f ++rkke+++ ie vGk+lra++++ lcl|NCBI__GCF_000016505.1:WP_012101468.1 293 WILENQTGRPSFIAKRKKEQNHPIEVVGKKLRAMMSW 329 ***********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (333 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.99 // [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