Align acetohydroxy-acid isomeroreductase subunit (EC 1.1.1.383) (characterized)
to candidate WP_013643698.1 METBO_RS00460 ketol-acid reductoisomerase
Query= metacyc::MONOMER-11920 (328 letters) >NCBI__GCF_000191585.1:WP_013643698.1 Length = 328 Score = 491 bits (1264), Expect = e-143 Identities = 233/328 (71%), Positives = 283/328 (86%) Query: 1 MKIYYENDIDMEILADKKIAVIGYGSQGEAQARNMADSGLNVIVGLRRGGSSWKKAHDDG 60 MK+YYE D+D++IL DK +AVIGYGSQG AQ+RNM +SGLNV+VGLR+ G+SW KA +DG Sbjct: 1 MKMYYEKDVDVDILKDKTVAVIGYGSQGMAQSRNMHESGLNVVVGLRKDGASWNKAKEDG 60 Query: 61 MNVMTIEDASREADIIHILIPDEIQETVFEQSIRPYLKEGNTISFSHGYNIHYGYIKAPE 120 + VMTIE+A+ +AD+IH+LIPDEIQ V+E+SI+ L+ GNTISFSHGYNIH+GYI P+ Sbjct: 61 LTVMTIEEAAAKADVIHVLIPDEIQAKVYEESIKDNLESGNTISFSHGYNIHFGYINPPK 120 Query: 121 GVNVTMVAPKGPGAMVRRTYLEGFGIPGLVAVEVDATGDAMEQALAMAKACGLARAGVLE 180 VN+TM+APKGPGAMVR+TY EGFG+PGL+A+E D TGDA + ALAM + GL RAGVLE Sbjct: 121 DVNITMIAPKGPGAMVRKTYEEGFGVPGLIAIERDYTGDAFKIALAMGQGSGLTRAGVLE 180 Query: 181 TTFREETETDLFGEQAVLCGGVTELINTAFKTLVRAGYQPEIAYFETCHELKLIVDLIYE 240 TTF+EETETDLFGEQ VLCGGVTELI F+TLV AGYQPEIAYFETCHE+KLIVDLIY Sbjct: 181 TTFKEETETDLFGEQVVLCGGVTELIAAGFQTLVDAGYQPEIAYFETCHEVKLIVDLIYA 240 Query: 241 RGFRGMWHNVSNTAEFGGLTRRGRIITEETEKEMDEILKEIQNGKFAKEWALENRAGAPM 300 +GF GMW++VSNTAE+GGL+RR RIIT+ET EM + L+EIQ G+FAKEW LEN+AG PM Sbjct: 241 KGFAGMWNDVSNTAEYGGLSRRKRIITDETRLEMKKALEEIQTGEFAKEWTLENQAGKPM 300 Query: 301 LKRMRKLESELEIEEVGSKLRKLCGLEK 328 L R+R +E+ L+IE+VGSKLRKLCGL+K Sbjct: 301 LNRLRAIEASLQIEKVGSKLRKLCGLQK 328 Lambda K H 0.317 0.136 0.390 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: 434 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: 328 Length of database: 328 Length adjustment: 28 Effective length of query: 300 Effective length of database: 300 Effective search space: 90000 Effective search space used: 90000 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_013643698.1 METBO_RS00460 (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.22556.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-148 478.6 1.3 4.2e-148 478.4 1.3 1.0 1 lcl|NCBI__GCF_000191585.1:WP_013643698.1 METBO_RS00460 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000191585.1:WP_013643698.1 METBO_RS00460 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 478.4 1.3 4.2e-148 4.2e-148 1 314 [] 14 328 .] 14 328 .] 0.99 Alignments for each domain: == domain 1 score: 478.4 bits; conditional E-value: 4.2e-148 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 lk+k+va+iGyGsqG aq++n+++sglnv+vglrk++asw+kA+edG+ v+t+eea++kad+i++L+pD lcl|NCBI__GCF_000191585.1:WP_013643698.1 14 LKDKTVAVIGYGSQGMAQSRNMHESGLNVVVGLRKDGASWNKAKEDGLTVMTIEEAAAKADVIHVLIPD 82 79******************************************************************* PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e+q +vye++ik++l+ g++++fsHG+ni+f +i++pkdv+++++APKgpGa+vR++y+eg+Gvp+liA lcl|NCBI__GCF_000191585.1:WP_013643698.1 83 EIQAKVYEESIKDNLESGNTISFSHGYNIHFGYINPPKDVNITMIAPKGPGAMVRKTYEEGFGVPGLIA 151 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 +e+d+tg+a +iAla+ ++ G +ragvlettFkeE+e+DLfGEq+vLcGg+++li a+f+tLv+aGyqp lcl|NCBI__GCF_000191585.1:WP_013643698.1 152 IERDYTGDAFKIALAMGQGSGLTRAGVLETTFKEETETDLFGEQVVLCGGVTELIAAGFQTLVDAGYQP 220 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++he+klivdl++ kG+++m++ vsntA++g+l++r +i+++e++ em+k l+eiq+Gefake lcl|NCBI__GCF_000191585.1:WP_013643698.1 221 EIAYFETCHEVKLIVDLIYAKGFAGMWNDVSNTAEYGGLSRRkRIITDETRLEMKKALEEIQTGEFAKE 289 *****************************************99************************** PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkaek 314 w+le++agkp++++ r e +iekvG++lr+l+ ++k lcl|NCBI__GCF_000191585.1:WP_013643698.1 290 WTLENQAGKPMLNRLRAIEASLQIEKVGSKLRKLCGLQK 328 **********************************98775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (328 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: 8.71 // [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