Align ketol-acid reductoisomerase (NAD+) (EC 1.1.1.382); ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_011613653.1 TERY_RS20915 ketol-acid reductoisomerase
Query= BRENDA::C8WR67 (344 letters) >NCBI__GCF_000014265.1:WP_011613653.1 Length = 331 Score = 437 bits (1123), Expect = e-127 Identities = 215/331 (64%), Positives = 266/331 (80%), Gaps = 1/331 (0%) Query: 1 MEKIYYDADISIQPLADKRIAVIGYGSQGHAHAQNLRDSGFDVVIGLRPGSSWA-KAEAD 59 M ++YYD+D ++ L DK IA+IGYGSQGHAHA NL+DSG V++GL GS A KA+ Sbjct: 1 MARMYYDSDANLDILNDKTIAIIGYGSQGHAHALNLKDSGSKVIVGLYSGSKSATKAKDA 60 Query: 60 GFRVMAVGEAVEESDVIMILLPDERQPAVYEREIRPYLTAGKALAFAHGFNIHFSQIQPP 119 G V V EA E++D+IMILLPDE Q VY+ +I P+L GK LAFAHGFNIHF QI PP Sbjct: 61 GLDVYPVDEAAEKADLIMILLPDEVQKTVYKNQIEPHLKEGKILAFAHGFNIHFGQIIPP 120 Query: 120 KDVDVFMVAPKGPGHLVRRVYEAGGGVPALIAVHQDASGQAKDLALAYARGIGAGRAGIL 179 ++VDV MVAPKGPGHLVRR YE G GVP L A+ QDASGQ +D A+AYA+GIG RAGIL Sbjct: 121 ENVDVVMVAPKGPGHLVRRTYEQGEGVPCLFAIFQDASGQGRDRAMAYAKGIGGTRAGIL 180 Query: 180 TTTFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPEIAYFECLHEMKLIVDLIY 239 TTFREETETDLFGEQ VLCGGLSALIKAGFETLV+AGYQPE+AYFECLHE+KLIVDL+ Sbjct: 181 ETTFREETETDLFGEQVVLCGGLSALIKAGFETLVKAGYQPELAYFECLHEVKLIVDLVV 240 Query: 240 EGGLEYMRYSISDTAQWGDFTSGPRIINEETKKEMRRILADIQSGAFAKSWILENQANRP 299 EGGL MR SIS+TA++GD+T GPRI+ +ET+ +M++IL++IQSG FA+ +++ENQ +P Sbjct: 241 EGGLANMRDSISNTAEFGDYTRGPRIVTDETRAQMQKILSEIQSGQFAREFVMENQTGKP 300 Query: 300 MFNAINRRELEHPIEVVGRKLRSMMPFIKAK 330 +F A+ R+E EH IE VG+ LR+M ++K + Sbjct: 301 VFTAMRRQEAEHSIEEVGKDLRAMFSWLKKR 331 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: 355 Number of extensions: 12 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_011613653.1 TERY_RS20915 (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.2824.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-151 489.7 0.2 1.7e-151 489.5 0.2 1.0 1 lcl|NCBI__GCF_000014265.1:WP_011613653.1 TERY_RS20915 ketol-acid reductoi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000014265.1:WP_011613653.1 TERY_RS20915 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 489.5 0.2 1.7e-151 1.7e-151 1 313 [. 15 328 .. 15 329 .. 0.99 Alignments for each domain: == domain 1 score: 489.5 bits; conditional E-value: 1.7e-151 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 l++k++aiiGyGsqG+a+alnl+dsg +vivgl+++++s +kA++ G++v v+ea++kadlimiLlpD lcl|NCBI__GCF_000014265.1:WP_011613653.1 15 LNDKTIAIIGYGSQGHAHALNLKDSGSKVIVGLYSGSKSATKAKDAGLDVYPVDEAAEKADLIMILLPD 83 689****************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 evqk+vy+++i+p lkegk+l f+HGfni+f qi +p++vdvv+vAPKgpG+lvR++y++g+Gvp l+A lcl|NCBI__GCF_000014265.1:WP_011613653.1 84 EVQKTVYKNQIEPHLKEGKILAFAHGFNIHFGQIIPPENVDVVMVAPKGPGHLVRRTYEQGEGVPCLFA 152 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 + qd++g++++ A+ayAk+iGg+rag+lettF+eE+e+DLfGEq+vLcGgl+alika+f+tLv+aGyqp lcl|NCBI__GCF_000014265.1:WP_011613653.1 153 IFQDASGQGRDRAMAYAKGIGGTRAGILETTFREETETDLFGEQVVLCGGLSALIKAGFETLVKAGYQP 221 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 elAyfe++he+klivdl+ e+Gl++mrd++sntA++g+++++ +i+++e++++mqkil eiq+G+fa+e lcl|NCBI__GCF_000014265.1:WP_011613653.1 222 ELAYFECLHEVKLIVDLVVEGGLANMRDSISNTAEFGDYTRGpRIVTDETRAQMQKILSEIQSGQFARE 290 ********************************************************************* PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkae 313 +++e+++gkp f+++r++e e++ie+vGk+lra++++ lcl|NCBI__GCF_000014265.1:WP_011613653.1 291 FVMENQTGKPVFTAMRRQEAEHSIEEVGKDLRAMFSWL 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.05 // [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