Align ketol-acid reductoisomerase (NAD+) (EC 1.1.1.382); ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_011317028.1 AVA_RS00670 ketol-acid reductoisomerase
Query= BRENDA::C8WR67 (344 letters) >NCBI__GCF_000204075.1:WP_011317028.1 Length = 331 Score = 448 bits (1152), Expect = e-130 Identities = 221/329 (67%), Positives = 266/329 (80%), Gaps = 1/329 (0%) Query: 1 MEKIYYDADISIQPLADKRIAVIGYGSQGHAHAQNLRDSGFDVVIGLRPGSSWA-KAEAD 59 M ++YYD D ++ LA K IA+IGYGSQGHAHA NL+DSG +V++GL PGS A KA+A Sbjct: 1 MARMYYDEDANLDLLAGKTIAIIGYGSQGHAHALNLKDSGLNVIVGLYPGSKSAEKAQAA 60 Query: 60 GFRVMAVGEAVEESDVIMILLPDERQPAVYEREIRPYLTAGKALAFAHGFNIHFSQIQPP 119 G V V +A +D IMILLPDE Q VY+ EI P L G LAFAHGFNIHF Q+ PP Sbjct: 61 GLTVKNVADAANVADFIMILLPDEVQKTVYKNEIEPNLQEGNTLAFAHGFNIHFGQVVPP 120 Query: 120 KDVDVFMVAPKGPGHLVRRVYEAGGGVPALIAVHQDASGQAKDLALAYARGIGAGRAGIL 179 +VDV MVAPKGPGHLVRR YE G GVPAL AV+QDASG+A+D AL+YA+GIG R G+L Sbjct: 121 ANVDVVMVAPKGPGHLVRRTYEQGQGVPALFAVYQDASGKARDRALSYAKGIGGTRGGVL 180 Query: 180 TTTFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPEIAYFECLHEMKLIVDLIY 239 TTFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPE+AYFECLHE+KLIVDL+ Sbjct: 181 ETTFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPELAYFECLHEVKLIVDLVV 240 Query: 240 EGGLEYMRYSISDTAQWGDFTSGPRIINEETKKEMRRILADIQSGAFAKSWILENQANRP 299 EGGL MR SIS+TA++GD+T GPRI+NE+TK EMR++L++IQSG FA+ ++LENQ+ +P Sbjct: 241 EGGLAKMRDSISNTAEYGDYTRGPRIVNEQTKAEMRKVLSEIQSGQFAREFVLENQSGKP 300 Query: 300 MFNAINRRELEHPIEVVGRKLRSMMPFIK 328 F A+ R+E EHPIE VG+ LR+M ++K Sbjct: 301 GFTAMRRQEAEHPIEEVGKDLRAMFSWLK 329 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: 389 Number of extensions: 13 Number of successful extensions: 2 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: 331 Length adjustment: 28 Effective length of query: 316 Effective length of database: 303 Effective search space: 95748 Effective search space used: 95748 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_011317028.1 AVA_RS00670 (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.840359.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-152 493.5 0.2 1.2e-152 493.3 0.2 1.0 1 NCBI__GCF_000204075.1:WP_011317028.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000204075.1:WP_011317028.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 493.3 0.2 1.2e-152 1.2e-152 1 313 [. 15 328 .. 15 329 .. 0.99 Alignments for each domain: == domain 1 score: 493.3 bits; conditional E-value: 1.2e-152 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 l+gk++aiiGyGsqG+a+alnl+dsglnvivgl+++++s +kA+ G+ v++v++a++ ad+imiLlpDevqk NCBI__GCF_000204075.1:WP_011317028.1 15 LAGKTIAIIGYGSQGHAHALNLKDSGLNVIVGLYPGSKSAEKAQAAGLTVKNVADAANVADFIMILLPDEVQK 87 689********************************************************************** PP TIGR00465 74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146 +vy++ei+p+l+eg++l f+HGfni+f q+v+p++vdvv+vAPKgpG+lvR++y++g+Gvp+l+Av+qd++g+ NCBI__GCF_000204075.1:WP_011317028.1 88 TVYKNEIEPNLQEGNTLAFAHGFNIHFGQVVPPANVDVVMVAPKGPGHLVRRTYEQGQGVPALFAVYQDASGK 160 ************************************************************************* PP TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219 a++ Al+yAk+iGg+r gvlettF+eE+e+DLfGEqavLcGgl+alika+f+tLveaGyqpelAyfe++he+k NCBI__GCF_000204075.1:WP_011317028.1 161 ARDRALSYAKGIGGTRGGVLETTFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPELAYFECLHEVK 233 ************************************************************************* PP TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291 livdl+ e+Gl++mrd++sntA++g+++++ +i++e++k+em+k+l eiq+G+fa+e++le++ gkp f+++r NCBI__GCF_000204075.1:WP_011317028.1 234 LIVDLVVEGGLAKMRDSISNTAEYGDYTRGpRIVNEQTKAEMRKVLSEIQSGQFAREFVLENQSGKPGFTAMR 306 ************************************************************************* PP TIGR00465 292 kkekeqeiekvGkelralvkae 313 ++e e+ ie+vGk+lra++++ NCBI__GCF_000204075.1:WP_011317028.1 307 RQEAEHPIEEVGKDLRAMFSWL 328 *******************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (331 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: 19.55 // [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