Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_013009760.1 DACET_RS02095 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >NCBI__GCF_000025725.1:WP_013009760.1 Length = 338 Score = 424 bits (1089), Expect = e-123 Identities = 201/338 (59%), Positives = 256/338 (75%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60 MK++Y+KD +L LIK K V +IGYGSQG+ H N+KDSGV+V V LR+ +SW KA AG Sbjct: 1 MKIYYEKDTNLELIKSKKVAVIGYGSQGYGHTNNMKDSGVDVCVALREGSSSWKKAEGAG 60 Query: 61 LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120 L+V EV EA K AD +M+L PDE D+YK + ++EG LAFAHGFN+ + ++P Sbjct: 61 LKVMEVKEACKWADFIMVLAPDECQGDIYKEAIEPGLEEGNYLAFAHGFNILFNQIVPPT 120 Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180 D++V+MIAPK PGH VRA Y +G GVP LIA+ Q+ +G +R++ALSYA A GG RA I+E Sbjct: 121 DVNVVMIAPKGPGHLVRAEYQKGAGVPCLIAIEQDYTGDSREMALSYANAIGGARAAILE 180 Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 T F+EETETDLFGEQ VLCGG +LI+ GFETL EAGYAPEMAY+ECLHE+KLIVDLIYE Sbjct: 181 TTFKEETETDLFGEQTVLCGGLAQLIQYGFETLTEAGYAPEMAYYECLHEVKLIVDLIYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300 GGI NM YSISN A+YG+ GPR++T E K+ MKQ L +IQ+G++A ++LENKA P Sbjct: 241 GGITNMRYSISNTAQYGDLTRGPRIITPEVKENMKQALYEIQSGQFANEWMLENKANCPN 300 Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 + R+ AEH IE+VG KLR +M W+ K K+VD+SKN Sbjct: 301 FHALTRMGAEHPIEKVGEKLRGLMSWLDKGKIVDKSKN 338 Lambda K H 0.316 0.133 0.379 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: 399 Number of extensions: 12 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: 338 Length adjustment: 28 Effective length of query: 310 Effective length of database: 310 Effective search space: 96100 Effective search space used: 96100 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_013009760.1 DACET_RS02095 (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.7005.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-140 453.8 0.1 1.5e-140 453.6 0.1 1.0 1 lcl|NCBI__GCF_000025725.1:WP_013009760.1 DACET_RS02095 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025725.1:WP_013009760.1 DACET_RS02095 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 453.6 0.1 1.5e-140 1.5e-140 1 312 [. 14 326 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 453.6 bits; conditional E-value: 1.5e-140 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 +k+kkva+iGyGsqG++++ n++dsg++v v+lr++++swkkAe G+kv++v+ea k ad+im+L pD lcl|NCBI__GCF_000025725.1:WP_013009760.1 14 IKSKKVAVIGYGSQGYGHTNNMKDSGVDVCVALREGSSSWKKAEGAGLKVMEVKEACKWADFIMVLAPD 82 689****************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e q + y++ i+p l+eg+ l f+HGfni f+qiv+p dv+vv++APKgpG+lvR ey++g+Gvp liA lcl|NCBI__GCF_000025725.1:WP_013009760.1 83 ECQGDIYKEAIEPGLEEGNYLAFAHGFNILFNQIVPPTDVNVVMIAPKGPGHLVRAEYQKGAGVPCLIA 151 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 +eqd+tg+++e+Al+yA+aiGgara +lettFkeE+e+DLfGEq+vLcGgl++li+ +f+tL+eaGy+p lcl|NCBI__GCF_000025725.1:WP_013009760.1 152 IEQDYTGDSREMALSYANAIGGARAAILETTFKEETETDLFGEQTVLCGGLAQLIQYGFETLTEAGYAP 220 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ay e++he+klivdl++e+G+++mr ++sntA++g+l+++ +i++ e+k++m++ l eiq+G+fa+e lcl|NCBI__GCF_000025725.1:WP_013009760.1 221 EMAYYECLHEVKLIVDLIYEGGITNMRYSISNTAQYGDLTRGpRIITPEVKENMKQALYEIQSGQFANE 289 ********************************************************************* PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312 w+le++a+ p+f++ ++ e+ iekvG++lr l+++ lcl|NCBI__GCF_000025725.1:WP_013009760.1 290 WMLENKANCPNFHALTRMGAEHPIEKVGEKLRGLMSW 326 *********************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (338 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: 7.18 // [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