Align Ketol-acid reductoisomerase (NADP(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.86 (characterized)
to candidate WP_092997330.1 BLP65_RS11785 ketol-acid reductoisomerase
Query= SwissProt::C1DFH7 (338 letters) >NCBI__GCF_900102855.1:WP_092997330.1 Length = 339 Score = 546 bits (1406), Expect = e-160 Identities = 265/338 (78%), Positives = 296/338 (87%) Query: 1 MKVYYDKDCDLSIIQSKKVAIIGYGSQGHAHACNLKDSGVDVYVGLRAGSASVAKAEAHG 60 M +YYDKDCDLSII+ KVAI+GYGSQGHAHA NLK+SGVDV V LR GS+S KAE+ G Sbjct: 2 MNIYYDKDCDLSIIRGMKVAIVGYGSQGHAHANNLKESGVDVTVALREGSSSAKKAESAG 61 Query: 61 LTVKSVKDAVAAADVVMILTPDEFQGRLYKDEIEPNLKKGATLAFAHGFSIHYNQVVPRA 120 LTVK+V +A AAD+VM+L PDE Q +Y I PNLK+GA LAFAHGF+IHYNQ+VPRA Sbjct: 62 LTVKAVDEACKAADLVMVLAPDENQAEIYNKSIAPNLKQGAVLAFAHGFNIHYNQIVPRA 121 Query: 121 DLDVIMIAPKAPGHTVRSEFVRGGGIPDLIAVYQDASGNAKNLALSYACGVGGGRTGIIE 180 DLDVIMIAPKAPGHTVRSEF RGGGIPDLIA++QDASG A+ +ALSYA +GGGRTGIIE Sbjct: 122 DLDVIMIAPKAPGHTVRSEFTRGGGIPDLIAIHQDASGKAREIALSYASAIGGGRTGIIE 181 Query: 181 TTFKDETETDLFGEQAVLCGGCVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMFE 240 TTFKDETETDLFGEQAVLCGG VELV+AGFETLV+AGYAPEMAYFECLHELKLIVDLM+E Sbjct: 182 TTFKDETETDLFGEQAVLCGGTVELVRAGFETLVDAGYAPEMAYFECLHELKLIVDLMYE 241 Query: 241 GGIANMNYSISNNAEYGEYVTGPEVINEQSRQAMRNALKRIQDGEYAKMFITEGAANYPS 300 GGIANMNYSISNNAEYGEYVTGP++IN+QSR AMR ALK IQ+GEYAK FI EG+ NYP Sbjct: 242 GGIANMNYSISNNAEYGEYVTGPKIINDQSRAAMREALKNIQNGEYAKRFILEGSTNYPE 301 Query: 301 MTAYRRNNAAHQIEVVGEKLRTMMPWIAANKIVDKTKN 338 MTA RRNNA H+IE GE+LR+MMPWI AN +VDK KN Sbjct: 302 MTAIRRNNAEHEIEKTGERLRSMMPWITANALVDKEKN 339 Lambda K H 0.317 0.134 0.388 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: 446 Number of extensions: 5 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: 338 Length of database: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 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_092997330.1 BLP65_RS11785 (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.24864.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-135 436.4 0.9 2.9e-135 436.2 0.9 1.0 1 lcl|NCBI__GCF_900102855.1:WP_092997330.1 BLP65_RS11785 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900102855.1:WP_092997330.1 BLP65_RS11785 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 436.2 0.9 2.9e-135 2.9e-135 2 312 .. 16 327 .. 15 329 .. 0.99 Alignments for each domain: == domain 1 score: 436.2 bits; conditional E-value: 2.9e-135 TIGR00465 2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDe 70 +g kvai+GyGsqG+a+a nl++sg++v+v+lr++++s kkAe G+ v+ v+ea k+adl+m+L pDe lcl|NCBI__GCF_900102855.1:WP_092997330.1 16 RGMKVAIVGYGSQGHAHANNLKESGVDVTVALREGSSSAKKAESAGLTVKAVDEACKAADLVMVLAPDE 84 6889***************************************************************** PP TIGR00465 71 vqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAv 139 q e y+++i+p+lk+g++l f+HGfni+++qiv+++d+dv+++APK+pG++vR+e+ +g G+p liA+ lcl|NCBI__GCF_900102855.1:WP_092997330.1 85 NQAEIYNKSIAPNLKQGAVLAFAHGFNIHYNQIVPRADLDVIMIAPKAPGHTVRSEFTRGGGIPDLIAI 153 ********************************************************************* PP TIGR00465 140 eqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpe 208 +qd++g+a+eiAl+yA aiGg+r g++ettFk+E+e+DLfGEqavLcGg +l++a+f+tLv+aGy+pe lcl|NCBI__GCF_900102855.1:WP_092997330.1 154 HQDASGKAREIALSYASAIGGGRTGIIETTFKDETETDLFGEQAVLCGGTVELVRAGFETLVDAGYAPE 222 ********************************************************************* PP TIGR00465 209 lAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakew 276 +Ayfe++helklivdl++e+G+++m ++sn A++g++ ++ +i++++ +++m++ lk+iqnGe+ak + lcl|NCBI__GCF_900102855.1:WP_092997330.1 223 MAYFECLHELKLIVDLMYEGGIANMNYSISNNAEYGEYVTGpKIINDQSRAAMREALKNIQNGEYAKRF 291 *****************************************9*************************** PP TIGR00465 277 alekeagkpafeearkkekeqeiekvGkelralvka 312 +le ++++p+++++r+ + e+eiek+G++lr ++++ lcl|NCBI__GCF_900102855.1:WP_092997330.1 292 ILEGSTNYPEMTAIRRNNAEHEIEKTGERLRSMMPW 327 **********************************98 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.58 // [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